New benzimidazoles derivatives as tec kinases family inhibitors

ABSTRACT

The present invention relates to a novel family of covalent kinases inhibitors. Compounds of this class have been found to have inhibitory activity against members of the Tec kinase family, particularly ITK, BTK, BMX, Tec and/or RLK. The present invention is directed to a compound of Formula I or pharmaceutically acceptable salt, solvate, solvate of salt, stereoisomer, tautomer, isotope, prodrug, complex or biologically active metabolite thereof, and its use in therapy.

FIELD OF INVENTION

The present invention relates to a novel family of protein kinaseinhibitors, their pharmaceutically acceptable salts, to pharmacologicalcompositions that contain them and to their use of the inhibitors totreat or prevent diseases, disorders and conditions associated withkinase function.

BACKGROUND OF THE INVENTION

Protein kinases are a large group of intracellular and transmembranesignalling proteins in eukaryotic cells (Manning G. et al, (2002)Science, 298: 1912-1934). Phosphorylation of specific amino acidresidues in target proteins by protein kinases can modulate theiractivity leading to profound changes in cellular signalling andmetabolism. Kinases play key roles in the regulation of cellularproliferation, survival, differentiation and function. Many kinases havebeen implicated in disease and, as such, are attractive therapeutictargets.

The Tec family of kinases consists of Tyrosine kinase expressed inhepatocellular carcinoma (TEC), Interleukin-2 inducible T-cell kinase(ITK, also known as TSK and EMT), Resting lymphocyte kinase (RLK, alsoknown as TXK), Bruton's tyrosine kinase (BTK), Bone marrow kinase on theX-chromosome (BMX, also known as ETK) (Bradshaw J M Cell Signal. 2010;22(8):1175-84). These intracellular kinases play important roles in thedevelopment and function of lymphocytes and myeloid cells (Horwood etal. Int Rev Immunol. 2012; 31(2):87-103, Felices M et al. Adv Immunol.2007; 93:145-84). Additionally, selected Tec family members such as ITK,TEC and BMX are expressed in cancerous cells where they may play a rolein cancer cell survival and malignancy (Carson C C et al. Clin CancerRes. 2015; 21(9):2167-76, Mano H. et al. Oncogene. 1990; 5(12):1781-6,Cenni B et al. Int Rev Immunol. 2012; 31(2):166-73).

ITK is an important component of T-cell signaling function anddifferentiation. ITK is activated upon stimulation of T-cell receptorsand initiates a signaling cascade that results in cellular activation,cytokine release and rapid proliferation. ITK is important in T-helper(Th) cell development and function including Th1, Th2, Th9, Th17 andT-regulatory cell development (Fowell D J et al. 1999 Immunity11:399-409; Gomez-Rodriguez J. et al. 2014 J. Exp Med 211:529-543,Gomez-Rodriguez J. et al 2016 Nat Commun. 2016; 7:10857). For example,ITK −/−CD4+ T-cells show significant reduction in the production of Th1and Th17 cytokines and exhibit skewed T− effector/Treg− cell ratios witha bias towards FoxP3+Treg (Kannan A et al 2015. J Neurosci. 35:221-233,Gomez-Rodriguez J. et al. 2014 J. Exp Med 211:529-543). Furthermore,specific inhibition of an allele-sensitive ITK mutant shows that ITK isimportant in Th1, Th2, Th17, and iNKT-cell cytokine production (Kannan Aet al Eur. J. Immunol. 2015. 45: 2276-2285). Consequently, ITK is animportant target for prevention or treatment of diseases involving Thcytokines, or where modulation of immunosuppressive Treg cells isdesired. Furthermore, polymorphisms in the ITK promoter that increaseITK expression in humans have been linked to increased asthma incidence(Lee, S. H. et al. 2011 Ann Hum Genet 75:359-369) and ITK preferentiallyregulates the secretion of the Th2 cytokines IL-5 and IL-13 in models ofallergic asthma suggesting that ITK inhibitors may be useful in thetreatment of asthma (Muller C et al. 2003 J Immunol. 170:5056-63). Also,ITK is upregulated in lesional skin from patients with allergic contactdermatitis, atopic dermatitis and psoriasis (von Bonin A et al. 2010.Exp. Derm; 20, 41-47).

RLK (TXK) is another Tec family member that is expressed in T-cells (HuQ et al. 1995 J. Biol Chem. 270:1928-1934). TXK and ITK regulate Thcell-mediated responses via their differential expression in Th1 and Th2cells, respectively (Sahu N et al. J. Immunol. 2008, 181:6125-6131).Furthermore, while ITK −/−mice have impaired in NKT cell generation thisdefect is exacerbated in the absence of both RLK and ITK (Felices M. etal. 2008, J Immunol. 180:3007-3018). Increased expression of RLK hasbeen reported in patients with Behcet's disease, an inflammatorydisorder associated with increased inflammation and Th1 cytokineproduction (Suzuki N et al. 2006 Clin Med Res. 4:147-151). Knockout ofboth ITK and RLK produces stronger effects on T-cell function thanknockout of either kinase alone (Schaeffer et al. 1999 Science284:638-641; Felices et al. 2008 J. Immunol. 180:3007-3018).

TEC kinase, first shown to be expressed in hepatocellular carcinoma(Mano et al. 1990 Oncogene. 5:1781-6), is expressed in normal B andT-cells and is up-regulated upon T-cell activation in Th1 and Th2 cells(Tomlinson M G et al 2004 Mol. Cell. Biol., 24:2455-2466). TEC may havedifferent roles from either ITK or RLK. TEC has a unique subcellulardistribution differential protein interactions compared with ITK and RLK(Tomlinson M G et al 2004 Mol. Cell. Biol., 24:2455-2466) and TEC, butnot RLK or LTK, is a tyrosine kinase of c-Maf leading to enhancement ofc-Maf-dependent IL-4 promoter activity (Liu C C et al. 2015 PLoS One.10:e0127617). Lastly, TEC controls assembly of the non-cannonicalcaspase 8 inflammasome involved in fungal sepsis and Tec-deficient miceare highly resistant to candidiasis (Zwolanek F et al. 2014 PLoS Pathog10, e1004525).

Experimental data using Tec-kinase family null animals supports thetherapeutic benefit of kinase inhibition in human disease. ITK modulatesneuroinflammation due to experimental autoimmune encephalomyelitis(EAE), the animal model of multiple sclerosis (MS). ITK−/− mice exhibitreduced disease severity, and transfer of ITK−/−CD4+ T-cells intoT-cell-deficient mice results in lower EAE disease severity (Kannan Aket al. J. Neurosci, 2015; 35:221-233). ITK −/− mice exhibit decreasedinflammatory response in contact hypersensitivity models (Von Bonin etal. Experimental Dermatology, 2010; 20, 41-47) and secretion of the Th2cytokines IL-5 and IL-13 is decreased in models of allergic asthma inITK −/− mice (Mueller C et al. J Immunol. 2003; 170(10):5056-63).

Data obtained with inhibitors of select Tec family kinases suggests thatinhibitors of these kinases may be useful in the treatment of disease.Inhibitors of ITK, RLK and other Tec family members may be useful in theprevention or treatment of T-cell related diseases such as multiplesclerosis, asthma, atopic dermatitis, psoriasis and inflammatory boweldiseases as well as viral infections. For example, a small moleculeinhibitor of ITK and RLK has shown efficacy in the mouse adoptive T-celltransfer model of colitis (Cho H-S et al. 2015; J. Immunol. 195:4822-31).

Also, a selective ITK inhibitor blocked leukocyte lung infiltrationfollowing ovalbumin challenge in a rat model of asthma (Lin T A et al.2004 Biochemistry. 43:11056-11062). Additionally, an ITK inhibitor waseffective in mouse models of skin contact hypersensitivity (von Bonin Aet al. 2010. Exp. Derm; 20, 41-47). Furthermore, ITK inhibitors canalter the HIV replication at various stages of viral life cycleincluding viral entry, gp120-induced actin reorganization, transcriptionfrom viral long terminal repeats (LTR) and virion assembly release fromT-cells (Readinger J A et al. Proc Natl Acad Sci USA. 2008;105(18):6684-9). Similarly ITK inhibition alleviates T-cell activationand murine myocardial inflammation associated with Coxsackie virus CVB3infection (He F et al. Mol Immunol. 2014; 59(1):30-8) and ITK isrequired for efficient replication of influenza virus in infectedT-cells (Fan K et al. J Gen Virol. 2012; 93(Pt 5):987-97). These datasuggest that inhibitors of the Tec family kinases may be useful in thetreatment of a variety of human and animal diseases.

SUMMARY OF THE INVENTION

The present invention relates to a novel family of covalent kinaseinhibitors. Compounds of this class have been found to have inhibitoryactivity against members of the Tec kinase family, particularly ITK,BTK, BMX and/or RLK (TXK) and/or TEC.

One aspect of the present invention is directed to a compound of FormulaI:

or pharmaceutically acceptable salt, solvate, solvate of salt,stereoisomer, tautomer, isotope, prodrug, complex or biologically activemetabolite thereof, wherein

R is selected from substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl;

L is independently selected from

where the ring B₁ is selected from substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl;

or

where the ring B₂ is selected from substituted or unsubstitutedpolycyclic ring system;

R¹ is selected from hydrogen, lower alkyl or lower cycloalkyl;

n is an integer from 0 to 1;

E is:

-   -   wherein:    -   Ra, Rb and Rc are independently selected from hydrogen, halogen,        —CN, substituted or unsubstituted alkyl, substituted or        unsubstituted heteroalkyl, substituted or unsubstituted        cycloalkyl, and substituted or unsubstituted heterocyclyl; or    -   Ra and Rb taken together with the carbon atoms to which they are        attached form a 3- to 8-membered substituted or unsubstituted        cycloalkyl ring, or form a 3- to 8-membered substituted or        unsubstituted heterocyclyl ring, and Rc is selected as above; or    -   Rb and Rc taken together with the carbon atom to which they are        attached form a 3- to 8-membered substituted or unsubstituted        cycloalkyl ring, or form a 3- to 8-membered substituted or        unsubstituted heterocyclyl ring, and Ra is selected as above; or    -   Ra and Rb taken together with the carbon atoms to which they are        attached form a triple bond and Rc is selected as above;

provided L-E is selected from

X is either:

-   -   1) selected from alkylene, -(alkylene)-NR²—, -(alkylene)-NR³—,        -(alkylene)-O—, —O—, —S—, —S(O)_(m)—, —NR²—, —NR³—, —C(O)—,        —C(O)O—, —C(O)NR²—, —C(O)ONR²—, or —S(O)_(m)NR²—;        -   R² is selected from hydrogen, lower alkyl or lower            cycloalkyl;        -   R³ is selected from —C(O)R⁴, —C(O)OR⁴ or —S(O)_(m)R⁴;        -   R⁴ is selected from lower alkyl or lower cycloalkyl; and        -   m is an integer selected from 1 to 2; or    -   2) X is a bond; and

Y is selected from hydrogen, halogen, substituted or unsubstitutedalkyl, substituted or unsubstituted alkenyl, substituted orunsubstituted alkynyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocyclyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted aralkyl, orsubstituted or unsubstituted heteroaralkyl.

In another aspect provided herein a pharmaceutical compositioncomprising a compound disclosed herein of Formula I, and/or apharmaceutically acceptable salt, solvate, solvate of salt,stereoisomer, tautomer, isotope, prodrug, complex or biologically activemetabolite thereof; and one or more pharmaceutically acceptableexcipients.

The pharmaceutical composition of the present invention comprising acompound of Formula I, and/or a pharmaceutically acceptable salt,solvate, solvate of salt, stereoisomer, tautomer, isotope, prodrug,complex or biologically active metabolite thereof suitable for use intherapy, wherein a subject is suffering of a disease, disorder orcondition in which one or more TEC kinase family member activity isimplicated and can be treated by kinase inhibition.

In another aspect, the present invention relates to the use of acompound of Formula I as defined herein, or a pharmaceuticallyacceptable salt or solvate thereof, in the manufacture of a medicamentfor use in subjects for the treatment or prevention of protein kinasemediated diseases or conditions, for the treatment of cancer, autoimmunediseases, allergic diseases, inflammatory diseases, graft-versus-hostdisease, thromboembolic diseases, neurological disorders, viralinfections, bone-related diseases or combinations thereof.

Another aspect of the present invention provides the synthetic methodsused to prepare compounds of Formula I of the present invention and arenot intended to be limiting.

In yet another aspect, provided herein a method of preventing ortreating a disease treatable by inhibition of ITK in a patient whichcomprises administering to the patient a pharmaceutical compositioncomprising a compound of Formula I and/or a pharmaceutically acceptablesalt, solvate, solvate of salt, stereoisomer, tautomer, isotope,prodrug, complex or biologically active metabolite thereof disclosedherein in a therapeutically effective amount and one or morepharmaceutically acceptable excipients. In a particular embodiment, thedisease or conditions include allergic diseases, autoimmune diseases,inflammatory diseases, thromboembolic diseases, bone-related diseases,cancer, graft-versus-host disease, and thereof.

In one embodiment of this aspect the patient suffers from a disease ordisorder that can be treated by kinase inhibition. The compounddisclosed herein and/or pharmaceutically acceptable salt thereof caninhibit one or more kinases including but not limited to ITK, RLK (alsoknown as TXK), BLK, BMX, BTK, JAK3, and/or TEC.

In another aspect the present invention provides a pharmaceuticalcombination comprising a compound of Formula I, Formula IIa, FormulaIIb, Formula IIc of the present invention or a pharmaceuticallyacceptable salt, solvate, solvate of salt, stereoisomer, tautomer,isotope, prodrug, complex or biologically active metabolite thereof andat least one additional active pharmaceutical ingredient for thetreatment or prevention of cancer, autoimmune diseases, allergicdiseases, inflammatory diseases or viral infection in combinationtherapy.

In one embodiment the present invention provides a method of treatmentwherein further comprising administering of a therapeutically effectiveamount of at least one additional active pharmaceutical ingredient forthe treatment of cancer, autoimmune diseases, allergic diseases,inflammatory diseases, neurological disorders or viral infection incombination therapy. The additional active pharmaceutical ingredient isadministered together with the compounds of Formula I, Formula IIa,Formula IIb, Formula IIc, or a pharmaceutically acceptable salt,solvate, solvate of salt, stereoisomer, tautomer, isotope, prodrug,complex or biologically active metabolite thereof as a single dosageform or separately as part of a multiple dosage form. The additionalactive pharmaceutical ingredient is selected from the group comprising:steroids, leukotriene antagonists, anti-histamines, anti-cancer,anti-viral, anti-biotic agents, protein kinase inhibitors orcombinations thereof.

The administration of a compound of the present invention may be by anyappropriate means known in the field, including systemic and localizedadministration. Prior to administration, the compounds may be formulatedas compositions suitable for pharmaceutical or clinical use. Suchcompositions may comprise appropriate carriers or excipients, such asthose for topical, inhalation, or systemic administration. The compoundof the present invention may be administered alone or in combinationwith one or more pharmaceutically acceptable active for the treatment orprevention of a protein kinase mediated condition.

All publications, patent applications, patents and other referencesmentioned herein are incorporated by reference in their entirety.

Other features, objects, and advantages of the invention(s) disclosedherein will be apparent from the description and drawings, and from theclaims.

DETAILED DESCRIPTION OF THE INVENTION

The present invention is directed to a compound of Formula I:

or pharmaceutically acceptable salt, solvate, solvate of salt,stereoisomer, tautomer, isotope, prodrug, complex or biologically activemetabolite thereof, wherein

R is selected from substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl;

L is independently selected from

where the ring B₁ is selected from substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl;

or

where the ring B₂ is selected from substituted or unsubstitutedpolycyclic ring system;

R¹ is selected from hydrogen, lower alkyl or lower cycloalkyl;

n is an integer from 0 to 1;

E is:

-   -   wherein:    -   Ra, Rb and Rc are independently selected from hydrogen, halogen,        —CN, substituted or unsubstituted alkyl, substituted or        unsubstituted heteroalkyl, substituted or unsubstituted        cycloalkyl, and substituted or unsubstituted heterocyclyl; or    -   Ra and Rb taken together with the carbon atoms to which they are        attached form a 3- to 8-membered substituted or unsubstituted        cycloalkyl ring, or form a 3- to 8-membered substituted or        unsubstituted heterocyclyl ring, and Rc is selected as above; or    -   Rb and Rc taken together with the carbon atom to which they are        attached form a 3- to 8-membered substituted or unsubstituted        cycloalkyl ring, or form a 3- to 8-membered substituted or        unsubstituted heterocyclyl ring, and Ra is selected as above; or    -   Ra and Rb taken together with the carbon atoms to which they are        attached form a triple bond and Rc is selected as above;

wherein L-E is selected from

X is either:

-   -   1) selected from alkylene, -(alkylene)-NR²—, -(alkylene)-NR³—,        -(alkylene)-O—, —O—, —S—, —S(O)_(m)—, —NR²—, —NR³—, —C(O)—,        —C(O)O—, —C(O)NR²—, —C(O)ONR²—, or —S(O)_(m)NR²—;    -   R² is selected from hydrogen, lower alkyl or lower cycloalkyl;    -   R³ is selected from —C(O)R⁴, —C(O)OR⁴ or —S(O)_(m)R⁴;    -   R⁴ is selected from lower alkyl or lower cycloalkyl; and    -   m is an integer selected from 1 to 2; or    -   2) X is a bond, and

Y is selected from hydrogen, halogen, substituted or unsubstitutedalkyl, substituted or unsubstituted alkenyl, substituted orunsubstituted alkynyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocyclyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted aralkyl, orsubstituted or unsubstituted heteroaralkyl.

An embodiment of the present invention relates to a novel covalentkinase inhibitors of Formula I

Wherein R is selected from substituted or unsubstituted 5- and6-membered aryl ring or substituted or unsubstituted 5- and 6-memberedheteroaryl ring;

L is independently selected from

-   -   Wherein ring B₁ is selected from substituted or unsubstituted 3-        to 8-membered cycloalkyl ring, substituted or unsubstituted 3-        to 8-membered heterocyclyl ring, substituted or unsubstituted 5-        and 6-membered aryl ring, substituted or unsubstituted 5- and        6-membered heteroaryl ring;    -   or

-   -   wherein ring B₂ is selected from substituted or unsubstituted 9-        to 12-membered polycyclic ring system;    -   R¹ is selected from hydrogen, C₁₋₆ alkyl or 3- to 8-membered        cycloalkyl ring;    -   n is an integer selected from 0 or 1;

E is selected from the group:

-   -   wherein Ra, Rb and Rc are independently selected from hydrogen,        halogen, —CN, substituted or unsubstituted C₁₋₆ alkyl chain,        substituted or unsubstituted heteroalkyl chain of 2 to 6 atoms,        substituted or unsubstituted 3- to 8-membered cycloalkyl ring,        or substituted or unsubstituted 3- to 8-membered heterocyclyl        ring; or    -   Ra and Rb taken together with the carbon atoms to which they are        attached form a 3- to 8-membered substituted or unsubstituted        cycloalkyl ring or form a 3- to 8-membered substituted or        unsubstituted heterocyclyl ring and Rc is selected as above; or    -   Rb and Rc taken together with the carbon atom to which they are        attached form a 3- to 8-membered substituted or unsubstituted        cycloalkyl ring, or form a 3- to 8-membered substituted or        unsubstituted heterocyclyl ring, and Ra is selected as above; or    -   Ra and Rb taken together with the carbon atoms to which they are        attached form a triple bond and Rc is selected as above;    -   wherein L-E is selected from

X is selected from C₁₋₆ alkylene, —(C₁₋₆ alkylene)-NR²—, —(C₁₋₆alkylene)-NR³—, —(C₁₋₆ alkylene)-O—, —O—, —S—, —S(O)_(m)—, —NR²—, —NR³—,—C(O)—, —C(O)O—, —C(O)NR²—, —C(O)ONR²—, and —S(O)_(m)NR²—;

wherein

-   -   R² is selected from hydrogen, C₁₋₆ alkyl or 3- to 8-membered        cycloalkyl ring;    -   R³ is selected from —C(O)R⁴, —C(O)OR⁴ and —S(O)_(m)R⁴;    -   R⁴ is selected from C₁₋₆ alkyl or 3- to 8-membered cycloalkyl        ring;    -   m is an integer selected from 1 to 2; or

X is a bond, and;

Y is selected from the group consisting of hydrogen, halogen,substituted or unsubstituted C₁₋₆ alkyl chain, substituted orunsubstituted C₂₋₆ alkenyl chain, substituted or unsubstituted C₂₋₆alkynyl chain, substituted or unsubstituted heteroalkyl chain of 2 to 6atoms, substituted or unsubstituted 3- to 8-membered cycloalkyl ring,substituted or unsubstituted 3- to 8-membered heterocyclyl ring,substituted or unsubstituted 5-, and 6-membered aryl ring, substitutedor unsubstituted 5-, and 6-membered heteroaryl ring, substituted orunsubstituted aralkyl, or substituted or unsubstituted heteroaralkyl.

An embodiment includes compounds of Formula I, wherein Ra, Rb and Rc areindependently selected from the group consisting of hydrogen, —CN,halogen, C₁₋₃ substituted or unsubstituted alkyl chain, or substitutedor unsubstituted heteroalkyl chain of 2 to 3 atoms.

An embodiment includes compounds of Formula I, wherein n is =0.

An embodiment includes compounds of Formula I, wherein n is =1.

An embodiment includes compounds of Formula I, wherein ring B₁ is a 3-to 8-membered substituted or unsubstituted cycloalkyl ring, or a 3- to8-membered substituted or unsubstituted heterocyclic ring.

An embodiment includes compounds of Formula I, wherein ring B₁ is asubstituted or unsubstituted aryl ring, or a substituted orunsubstituted heteroaryl ring, for example a substituted orunsubstituted phenyl ring or a substituted or unsubstituted 5 to 6membered heteroaryl ring.

An embodiment includes compounds of Formula I, wherein ring B₁ is asubstituted or unsubstituted 5-, and 6-membered aryl ring, or asubstituted or unsubstituted 5-, and 6-membered heteroaryl ring.

An embodiment includes compounds of Formula I, wherein ring B₁ is asubstituted or unsubstituted 6-membered aryl ring, for example asubstituted or unsubstituted phenyl ring.

An embodiment includes compounds of Formula I, wherein ring B₁ is asubstituted or unsubstituted cycloalkyl ring.

In an embodiment of the present invention B₁ is selected fromsubstituted or unsubstituted: cyclobutyl, cyclopentyl or cyclohexyl andn is 0.

In an alternate embodiment, B₁ is selected from substituted orunsubstituted phenyl, and n is 0.

An embodiment includes compounds of Formula I where R¹ is hydrogen ormethyl.

An embodiment includes compounds of Formula I, wherein R¹ is hydrogen.

An embodiment includes compounds of Formula I, wherein R¹ is methyl.

An embodiment includes compounds of Formula I, wherein B₂ is asubstituted or unsubstituted polycyclic ring system, for example a 9- or10-membered polycyclic ring system.

In an embodiment of the present invention B₂ is:

wherein B₃ is a 3- to 8-membered substituted or unsubstitutedheterocyclyl ring.

B₃ may also be a 5- or 6-membered substituted or unsubstitutedheterocyclyl ring. Optionally, B₃ is pyrolidine, morpholine, piperidine,or piperazine.

Preferably B₃ is pyrolidine or morpholine. Accordingly, B₂ may be:

An embodiment includes compounds of Formula I, wherein n is =0.

An embodiment includes compounds of Formula I, wherein n is =1.

An embodiment includes compounds of Formula I, wherein R is asubstituted or unsubstituted 6-membered aryl ring, for example asubstituted or unsubstituted phenyl ring.

An embodiment includes compounds of Formula I, wherein R is asubstituted or unsubstituted 5- or 6-heteroaryl ring.

An embodiment includes compounds of Formula I, wherein R is asubstituted or unsubstituted 5-membered heteroaryl ring.

An embodiment includes compounds of Formula I, wherein R is asubstituted or unsubstituted 6-membered heteroaryl ring.

An embodiment includes compounds of formula I where X—Y is selected from—CH₂—NH—Y, —CH₂—NR²—Y, —C(O)—NR²—Y, —NR²C(O)—Y, —NR²SO₂—Y, —O—CH₂—Y,—CH₂— NR³—Y, —CH₂—Y wherein Y is as defined herein.

An embodiment includes compounds of Formula I, where X—Y is selectedfrom —CH₂—NH—Y, and wherein Y is as defined herein.

An embodiment includes compounds of Formula I, where X—Y is selectedfrom —CH₂—NR²—Y, and wherein R² and Y are as defined herein.

An embodiment includes compounds of Formula I, where X—Y is selectedfrom —C(O)—NR²—Y, and wherein R² and Y are as defined herein.

An embodiment includes compounds of Formula I, where X—Y is selectedfrom —NR²C(O)—Y, and wherein R² and Y are as defined herein.

An embodiment includes compounds of Formula I, where X—Y is selectedfrom —NR²SO₂—Y, and wherein R² and Y are as defined herein.

An embodiment includes compounds of Formula I, where X—Y is selectedfrom —O—CH₂—Y, and wherein Y is as defined herein.

An embodiment includes compounds of Formula I, where X—Y is selectedfrom —CH₂—NR³—Y, and wherein R³ and Y are as defined herein.

An embodiment includes compounds of Formula I, where X—Y is selectedfrom —CH₂—Y, and wherein Y is as defined herein.

In an embodiment of the present invention B₁ is selected fromsubstituted or unsubstituted: cyclobutyl, cyclopentyl, cyclohexyl orphenyl.

In an alternate embodiment, B₁ is selected from substituted orunsubstituted: cyclobutyl, cyclopentyl, cyclohexyl or phenyl, and n is0.

More preferred embodiment includes compounds of Formula I where, whereinL-E is selected from the group consisting of:

An embodiment includes compounds of Formula I where L-E is selected fromthe group consisting of:

An alternate embodiment includes compounds of Formula I, wherein L-E isselected from:

An embodiment of the present invention includes compounds of Formula Iwhere L-E is selected from:

An embodiment of the present invention also includes compounds ofFormula I wherein E is selected from:

An embodiment of the present invention includes compounds of Formula I,where E is

An alternate embodiment includes compounds of Formula I, where X—Y isselected from:

An embodiment of the present invention includes compounds of Formula I,where X—Y is selected from:

An embodiment of the present invention includes compounds of Formula I,where X—Y is selected from:

An embodiment of the present invention includes compounds of Formula I,wherein X—Y is

An embodiment of the present invention includes compounds of Formula I,wherein X—Y is selected from:

An embodiment of the present invention compounds of Formula I, whereinX—Y is selected from:

An embodiment of the present invention includes compounds of Formula I,wherein X—Y is selected from:

An embodiment of the present invention includes compounds of Formula I,wherein X—Y is

An embodiment of the present invention includes compounds of Formula Iwhere, wherein R is selected from the group consisting of:

An embodiment of the present invention includes compounds of Formula Iwhere R is selected from:

An embodiment of the present invention includes compounds of Formula I,wherein R is selected from the group consisting of:

An embodiment of the present invention includes a compound having thechemical structure of Formula IIa

wherein

R is selected from substituted or unsubstituted 5- and 6-membered arylring or substituted or unsubstituted 5- and 6-membered heteroaryl ring;

X—Y is selected from the group consisting of: —CH₂—NH—Y, —CH₂—NR²—Y,—CH₂—NR³—Y, —NR²C(O)—Y, —C(O)NR²—Y, or —CH₂—Y;

wherein

-   -   R² is selected from hydrogen, C₁₋₆ alkyl chain or 3- to        8-membered cycloalkyl ring;    -   R³ is selected from —C(O)R⁴, —C(O)OR⁴ or —S(O)_(m)R⁴; wherein m        is an integer from 1 to 2;    -   R⁴ is selected from C₁₋₆ alkyl chain or 3- to 8-membered        cycloalkyl ring;    -   Y is selected from the group consisting of hydrogen, halogen,        substituted or unsubstituted C₁₋₆ alkyl chain, substituted or        unsubstituted C₂₋₆ alkenyl chain, substituted or unsubstituted        C₂₋₆ alkynyl chain, substituted or unsubstituted heteroalkyl        chain of 2 to 6 atoms, substituted or unsubstituted 3- to        8-membered cycloalkyl ring, substituted or unsubstituted 3- to        8-membered heterocyclyl ring, substituted or unsubstituted 5-,        and 6-membered aryl ring, substituted or unsubstituted 5-, and        6-membered heteroaryl ring, substituted or unsubstituted        aralkyl, or substituted or unsubstituted heteroaralkyl;

n₁ is an integer from 0 to 3;

n₂ is an integer from 1 to 3; and

R¹ is selected from hydrogen, C₁₋₆ alkyl chain or 3- to 8-memberedcycloalkyl ring.

The compound of Formula IIa is preferably the compound represented byFormula IIa or a pharmaceutically acceptable salt or solvate thereof. Itmay just be the simple compound of Formula IIa in one embodiment.

An embodiment of the present invention includes a compound having thechemical structure of Formula IIb

wherein

R is selected from substituted or unsubstituted 5- and 6-membered arylring or substituted or unsubstituted 5- and 6-membered heteroaryl ring;

X—Y is selected from the group consisting of: —CH₂—NH—Y, —CH₂—NR²—Y,—CH₂—NR³—Y, —NR²C(O)—Y, —C(O)NR²—Y, or —CH₂—Y;

wherein

-   -   R² is selected from hydrogen, C₁₋₆ alkyl chain or 3- to        8-membered cycloalkyl ring;    -   R³ is selected from —C(O)R⁴, —C(O)OR⁴ or —S(O)_(m)R⁴; wherein m        is an integer from 1 to 2;    -   R⁴ is selected from C₁₋₆ alkyl chain or 3- to 8-membered        cycloalkyl ring;    -   Y is selected from the group consisting of hydrogen, halogen,        substituted or unsubstituted C₁₋₆ alkyl chain, substituted or        unsubstituted C₂₋₆ alkenyl chain, substituted or unsubstituted        C₂₋₆ alkynyl chain, substituted or unsubstituted heteroalkyl        chain of 2 to 6 atoms, substituted or unsubstituted 3- to        8-membered cycloalkyl ring, substituted or unsubstituted 3- to        8-membered heterocyclyl ring, substituted or unsubstituted 5-,        and 6-membered aryl ring, substituted or unsubstituted 5-, and        6-membered heteroaryl ring, substituted or unsubstituted        aralkyl, or substituted or unsubstituted heteroaralkyl;

X¹ is selected from hydrogen or halogen; and

R¹ is selected from hydrogen, C₁₋₆alkyl chain or 3- to 8-memberedcycloalkyl ring.

The compound of Formula IIb is preferably the compound represented byFormula IIb or a pharmaceutically acceptable salt or solvate thereof. Itmay just be the simple compound of Formula IIb in one embodiment.

An embodiment of the present invention includes a compound having thechemical structure of Formula IIc

wherein

R is selected from substituted or unsubstituted 5- and 6-membered arylring or substituted or unsubstituted 5- and 6-membered heteroaryl ring;

X—Y is selected from the group consisting of:

-   -   CH₂—NH—Y, —CH₂—NR²—Y, —CH₂—NR³—Y, —NR²C(O)—Y, —C(O)NR²—Y, or        —CH₂—Y;

wherein

-   -   R² is selected from hydrogen, C₁₋₆ alkyl chain or 3- to        8-membered cycloalkyl ring;    -   R³ is selected from —C(O)R⁴, —C(O)OR⁴ or —S(O)_(m)R⁴; wherein m        is an integer from 1 to 2;    -   R⁴ is selected from C₁₋₆ alkyl chain or 3- to 8-membered        cycloalkyl ring;    -   Y is selected from the group consisting of hydrogen, halogen,        substituted or unsubstituted C₁₋₆ alkyl chain, substituted or        unsubstituted C₂₋₆ alkenyl chain, substituted or unsubstituted        C₂₋₆ alkynyl chain, substituted or unsubstituted heteroalkyl        chain of 2 to 6 atoms, substituted or unsubstituted 3- to        8-membered cycloalkyl ring, substituted or unsubstituted 3- to        8-membered heterocyclyl ring, substituted or unsubstituted 5-,        and 6-membered aryl ring, substituted or unsubstituted 5-, and        6-membered heteroaryl ring, substituted or unsubstituted        aralkyl, or substituted or unsubstituted heteroaralkyl; and

ring B₃ is a 3- to 8-membered substituted or unsubstituted heterocyclicring.

The compound of Formula IIc is preferably the compound represented byFormula IIc or a pharmaceutically acceptable salt or solvate thereof. Itmay just be the simple compound of Formula IIc in one embodiment.

Compounds of Formula I can exist as tautomers. For example, compounds ofFormula I can exist in the following tautomeric forms and bothtautomeric forms comprise part of the present invention:

wherein R, X, Y, L and E are as defined above.

In an embodiment of the present invention compounds are selected fromthe group consisting of

and pharmaceutically acceptable salts, solvates, solvate of salts,stereoisomers, tautomers, isotopes, prodrugs, and complex orbiologically active metabolites thereof.

The compounds of the present invention may have activity as inhibitorsof protein kinases including tyrosine protein kinases. Mostparticularly, compounds of the present invention may inhibit ITK enzymeand ITK-dependent cellular functions.

In an embodiment of the present invention compounds of Formula I may beformulated into a pharmaceutical composition which comprises aneffective amount of a compound of the present invention with apharmaceutically acceptable diluent or carrier.

According to the present invention there is provided a pharmaceuticalcomposition which comprises a compound of Formula I, or apharmaceutically acceptable salt or solvate thereof, in association withat least one pharmaceutically acceptable excipient, diluent or carrier.

The pharmaceutical compositions may be in a conventional pharmaceuticalform suitable for oral administration (e.g., tablets, capsules,granules, powders and syrups), parenteral administration (e.g.,injections (intravenous, intramuscular, or subcutaneous)), drop infusionpreparations, inhalation, eye lotion, topical administration (e.g.,ointment), or suppositories.

Regardless of the route of administration selected, the compounds may beformulated into pharmaceutically acceptable dosage forms by conventionalmethods known to those skilled in the art.

The term “compound” refers also to its pharmaceutically acceptable salt,solvate, solvate of salt, stereoisomer, tautomer, isotope, prodrug,complex or biologically active metabolite thereof.

The term “pharmaceutically effective amount” refers to any amount of thecomposition for the prevention and treatment of humans that is effectivein preventing or treating a disease or condition associated with proteinkinase activity.

The phrase “pharmaceutically acceptable” is employed herein to refer tothose ligands, materials, compositions, and/or dosage forms which are,within the scope of sound medical judgment, suitable for use in contactwith the tissues of human beings and animals without excessive toxicity,irritation, allergic response, or other problem or complication,commensurate with a reasonable benefit/risk ratio.

The phrase “pharmaceutically acceptable carrier” as used herein means apharmaceutically acceptable material, composition, or vehicle, such as aliquid or solid filler, diluent, excipient, solvent or encapsulatingmaterial. Each carrier must be acceptable in the sense of beingcompatible with the other ingredients of the formulation, including theactive ingredient, and not injurious or harmful to the patient. Someexamples of materials which can serve as pharmaceutically acceptablecarriers include: (1) sugars, such as lactose, glucose, and sucrose; (2)starches, such as corn starch, potato starch, and substituted orunsubstituted β-cyclodextrin; (3) cellulose, and its derivatives, suchas sodium carboxymethyl cellulose, ethyl cellulose, and celluloseacetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) talc; (8)excipients, such as cocoa butter and suppository waxes; (9) oils, suchas peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil,corn oil, and soybean oil; (10) glycols, such as propylene glycol; (11)polyols, such as glycerin, sorbitol, mannitol, and polyethylene glycol;(12) esters, such as ethyl oleate and ethyl laurate; (13) agar; (14)buffering agents, such as magnesium hydroxide and aluminum hydroxide;(15) alginic acid; (16) pyrogen-free water; (17) isotonic saline; (18)Ringer's solution; (19) ethyl alcohol; (20) phosphate buffer solutions;and (21) other non-toxic compatible substances employed inpharmaceutical formulations. For oral formulations, “pharmaceuticallyacceptable carrier” such as cellulose, calcium silicate, corn starch,lactose, sucrose, dextrose, calcium phosphate, stearic acid, magnesiumstearate, calcium stearate, gelatin, talc, surfactants, suspendingagents, emulsifiers, diluents, and others may be used. For injectableformulations, “pharmaceutically acceptable carrier” such as water,saline, glucose solution, glucose solution analogs, alcohols, glycols,ethers (e.g., polyethylene glycol 400), oils, fatty acids, fatty acidesters, glycerides, surfactants, suspending agents, emulsifiers, andothers may be used.

The term “pharmaceutically acceptable salt” refers to the relativelynon-toxic, inorganic and organic acid addition salts of the compound(s).These salts can be prepared in situ during the final isolation andpurification of the compound(s), or by separately reacting a purifiedcompound(s) in its free base form with a suitable organic or inorganicacid, and isolating the salt thus formed. Representative salts includethe hydrobromide, hydrochloride, sulfate, bisulfate, phosphate, nitrate,acetate, valerate, oleate, palmitate, stearate, laurate, benzoate,lactate, phosphate, tosylate, citrate, maleate, fumarate, succinate,tartrate, naphthylate, mesylate, glucoheptonate, lactobionate,laurylsulphonate salts, and amino acid salts, and the like (See, forexample, Berge et al. (1977) “Pharmaceutical Salts”, J. Pharm. Sci. 66:1-19).

In other cases, the compounds of the present invention may contain oneor more acidic functional groups and, thus, are capable of formingpharmaceutically acceptable salts with pharmaceutically acceptablebases. The term “pharmaceutically acceptable salts” in these instancesrefers to the relatively non-toxic inorganic and organic base additionsalts of a compound(s). These salts can likewise be prepared in situduring the final isolation and purification of the compound(s), or byseparately reacting the purified compound(s) in its free acid form witha suitable base, such as the hydroxide, carbonate, or bicarbonate of apharmaceutically acceptable metal cation, with ammonia, or with apharmaceutically acceptable organic primary, secondary, or tertiaryamine. Representative alkali or alkaline earth salts include thelithium, sodium, potassium, calcium, magnesium, and aluminum salts, andthe like. Representative organic amines useful for the formation of baseaddition salts include ethylamine, diethylamine, ethylenediamine,ethanolamine, diethanolamine, piperazine, and the like (see, forexample, Berge et al., supra).

As used herein, the term “affinity tag” means a ligand or group, linkedeither to a compound of the present invention or to a protein kinasedomain, that allows the conjugate to be extracted from a solution.

The term “spirocycle”, as used herein, refers to bicyclic rings systemconnected through just one atom. The rings can be different oridentical. The connecting atom, also called spiroatom, is preferably aquaternary carbon. Spirocycle may be optionally substituted with one ormore substituents as defined herein.

The term “alkyl”, as used herein, refers to a saturated hydrocarbonchain. Alkyl chains may be straight or branched. Alkyl chains may beoptionally substituted with one or more substituents as defined herein.Representative alkyl groups include methyl, ethyl, propyl, (n-propyl andisopropyl) butyl (n-butyl, t-butyl and isobutyl), pentyl (n-pentyl andisopentyl), hexyl and the like. In certain preferred embodiments, alkylsubstituents are lower alkyl groups, e.g., having from 1 to 6 carbonatoms, and in certain embodiments having C₁ to C₃ carbon atoms.

The term “alkenyl”, as used herein, refers to an unsaturated hydrocarbonchain analogous in length and possible substitution to the “alkyl”described above, but that contain at least one double bond.Representative alkenyl groups include vinyl, propen-2-yl, crotyl,isopenten-2-yl, 1,3-butadien-2-yl, 2,4-pentadienyl, and1,4-pentadien-3-yl. In certain preferred embodiments, alkenylsubstituents are lower alkenyl groups, e.g., having from 2 to 6 carbonatoms.

The term “alkynyl”, as used herein, refers to an unsaturated hydrocarbonchain analogous in length and possible substitution to the “alkyl”described above, but that contain at least one triple bond.Representative alkynyl groups include ethynyl, 1- and 3-propynyl, and3-butynyl. In certain preferred embodiments, alkynyl substituents arelower alkyl groups, e.g., having from 2 to 6 carbon atoms.

The term, “alkylene”, as used herein, refers to an alkyl group with twoopen valencies.

The term “heteroalkyl”, as used herein, refers to a saturated orpartially saturated chain containing one to four heteroatoms selectedfrom the group consisting of O, N and S, and wherein the nitrogen andsulfur atoms may optionally be oxidized and the nitrogen atom mayoptionally be quaternized. Heteroalkyl chains may be straight orbranched. Heteroalkyl chains may be optionally substituted with one ormore substituents as defined herein. The heteroatom(s) O, N and S may beplaced at any interior position of the heteroalkyl group. Up to twoheteroatoms may be consecutive.

The term “cycloalkyl”, as used herein, alternatively “carbocycle” and“carbocyclyl” refers to a saturated or partially saturated non-aromaticring, more preferably 3- to 8-membered ring, in which each atom of thering is carbon or; refers to a spirocycle where each ring is a saturatedor partially saturated hydrocarbon ring and the spiro atom is carbon.Cycloalkyl rings may be optionally substituted with one or moresubstituents as defined herein. The term “cycloalkyl”, “carbocycle” or“carbocyclyl” also include polycyclic ring systems having two or morecyclic rings in which two or more carbons are common to two adjoiningrings wherein at least one of the rings is cycloalkyl, e.g., the othercyclic rings can be aryls, heteroaryls, and/or heterocyclyls.Representative cycloalkyl rings include cyclopropyl, cyclobutyl,cyclopentyl, cyclohexyl, 1-cyclohexenyl, 3-cyclohexen-1-yl, cycloheptyl,tetrahydronaphthyl, indanyl, adamantly and combinations thereof.

The term “heterocyclyl” alternatively “heterocyclic”, as used herein,refers to non-aromatic ring structures, more preferably 3- to 8-memberedrings, whose ring structures include one to four heteroatoms or; refersto a spirocycle where the bicyclic rings system contains 1 to 4heteroatoms. Heterocyclyl rings may be optionally substituted with oneor more substituents as defined herein. The term “heterocyclyl” or“heterocyclic” also include polycyclic ring systems having two or morecyclic rings in which two or more carbons are common to two adjoiningrings wherein at least one of the rings is heterocyclic, e.g., the othercyclic rings can be cycloalkyls, aryls and/or heteroaryls. Heterocyclylgroups include, for example, tetrahydrofuran, piperidine, piperazine,pyrrolidine, morpholine, lactones, lactams and combinations thereof.

The term “aryl”, as used herein, refers to 5-, 6-, and 7-memberedaromatic rings in which each atom of the ring is carbon. Aryl rings maybe optionally substituted with one or more substituents as definedherein. The term “aryl” also includes polycyclic ring systems having twoor more cyclic rings in which two or more carbons are common to twoadjoining rings wherein at least one of the rings is aryl, e.g., theother cyclic rings can be cycloalkyls, heteroaryls, and/orheterocyclyls. Aryl groups include, for example, benzene, naphthalene,phenanthrene, anthracene and combinations thereof.

The term “heteroaryl” as used herein, refers to 5-, 6-, and 7-memberedaromatic rings whose ring structures include one to four heteroatoms.Heteroaryl rings may be optionally substituted with one or moresubstituents as defined herein. The term “heteroaryl” also includespolycyclic ring systems having two or more cyclic rings in which two ormore carbons are common to two adjoining rings wherein at least one ofthe rings is heteroaryl, e.g., the other cyclic rings can becycloalkyls, aryls and/or heterocyclyls. Heteroaryl groups include, forexample, pyrrole, furan, thiophene, imidazole, isoxazole, oxazole,thiazole, triazole, pyrazole, pyridine, pyrazine, pyridazine andpyrimidine, and combinations thereof.

The terms “polycyclyl” alternatively “polycyclic”, as used herein, referto two or more rings (e.g., cycloalkyls, aryls, heteroaryls, and/orheterocyclyls) in which two or more carbons are common to two adjoiningrings, e.g., the rings are “fused rings”. Polycyclyl rings may beoptionally substituted with one or more substituents as defined herein.

The term “aralkyl”, as used herein, refers to an alkyl group substitutedwith an aryl group, for example —(CH₂)_(p)—Ar and p is an integer from 1to 8 and Ar may be selected from any suitable aryl ring system, forexample phenyl or napthyl. For example “aralkyl” may be benzyl.

The term “heteroaralkyl”, as used herein, refers to an alkyl groupsubstituted with a heteroaryl group, for example —(CH₂)_(p)—Het and p isan integer from 1 to 8 and Het is any suitable heteroaryl ring system,such as those discussed in the above paragraphs.

The term “alkoxy”, as used herein, refers to an alkyl ether substituent,wherein the term alkyl is as defined above. Representative alkoxy groupsinclude methoxy, ethoxy, propoxy, tert-butoxy and combinations thereof.

The term “ether”, as used herein, refers to an oxy group bridging twomoieties linked at carbon atoms.

The term “alkoxyalkyl”, as used herein, refers to an alkyl groupsubstituted with an alkoxy group, thereby forming ether.

The term “halo” or “halogen”, as used herein, refers to fluorine,chlorine, bromine and iodine.

The term “heteroatom”, as used herein, refers to an atom of any elementother than carbon or hydrogen. Preferred heteroatoms are nitrogen,oxygen, and sulfur.

The term “hydrocarbon”, as used herein, refers to a group consistingentirely of carbon and hydrogen.

The term “haloalkyl”, as used herein, refers to an alkyl substituentwherein one or more hydrogens are replaced by a halogen.

The term “carbonyl”, as used herein, when alone includes formyl —CH(O)and in combination is a —C(O) group.

The term “carboxyl”, alternatively “carboxy”, as used herein, refers to—C(O)OH or the corresponding “carboxylate” anion, such as in acarboxylic acid salt.

The term “acyl”, as used herein, refers to —C(O)R wherein R is alkyl,heteroalkyl, haloalkyl, cycloalkyl, heterocyclyl, aryl or heteroaryl asdefined above. Representative acyl groups include acetyl,trifluoroacethyl, benzoyl, and the combinations thereof.

The term “alkoxycarbonyl”, as used herein, refers to —C(O)OR wherein Ris alkyl as defined above. Representative alkoxycarbonyl groups includemethoxycarbonyl, ethoxycarbonyl, and the combinations thereof.

The term “alkylthio”, as used herein, refers to a thioether —SR whereinR is alkyl as defined above. Representative alkylthio groups includemethylthio, ethylthio and combinations thereof.

The term “sulfonate”, as used herein, refers to a salt or ester of asulfonic acid —OSO₂R wherein R is alkyl, heteroalkyl, haloalkyl,cycloalkyl, heterocyclyl, aryl or heteroaryl as defined above.Representative sulfonate groups include mesylate, besylate, tosylate,and combinations thereof.

The term “sulfonyl”, as used herein, refers to —SO₂R wherein R is alkyl,heteroalkyl, haloalkyl, cycloalkyl, heterocyclyl, aryl or heteroaryl asdefined above. Representative sulfonate groups include methylsufonyl,ethylsulfonyl, and combinations thereof.

The term “sulfamoyl”, as used herein, refers to —SO₂NH₂.

The term “sulfonamido”, as used herein, refers to —S(O)₂NRR′ wherein Rand R′ are independently selected from alkyl, heteroalkyl, haloalkyl,cycloalkyl, heterocyclyl, aryl and heteroaryl as defined above. R and R′may combine to form a heterocyclyl ring.

The term “amino”, as used herein, refers to —NRR′ wherein R and R′ areindependently selected from hydrogen, alkyl, heteroalkyl, haloalkyl,cycloalkyl, heterocyclyl, aryl and heteroaryl as defined above. R and R′may combine to form a heterocyclyl ring.

The term “amido” alternatively “amide”, as used herein, refers to—C(O)NRR′ wherein R and R′ are independently selected from hydrogen,alkyl, heteroalkyl, haloalkyl, cycloalkyl, heterocyclyl, aryl orheteroaryl as defined above. R and R′ may combine to form anheterocyclyl ring.

The term “substituted” refers to moieties having substituents replacinghydrogen on one or more atoms of the backbone. It will be understoodthat “substitution” or “substituted with” includes the implicit provisothat such substitution is in accordance with permitted valence of thesubstituted atom and the substituent, and that the substitution resultsin a stable compound, e.g., which does not spontaneously undergotransformation such as by rearrangement, cyclization, elimination, etc.As used herein, the term “substituted” is contemplated to include allpermissible substituents of organic compounds. The permissiblesubstituents can be one or more and the same or different forappropriate organic compounds. For purposes of this invention, theheteroatoms such as nitrogen may have hydrogen substituents and/or anypermissible substituents of organic compounds described herein whichsatisfy the valences of the heteroatoms.

Substituents can include, for example, an alkyl, an alkenyl, an alkynyl,a haloalkyl, a heteroalkyl, a cycloalkyl, a heterocyclyl, an aryl, aheteroaryl, a halogen, a hydroxyl, a carbonyl, carboxyl, analkoxycarbonyl, a formyl, or an acyl, a thiocarbonyl (such as athioester, a thioacetate, or a thioformate), an alkoxy, a phosphoryl, aphosphate, a phosphonate, a phosphinate, an amino, an amido, an amidine,an imine, a cyano, a nitro, an azido, a sulfhydryl, an alkylthio, asulfate, a sulfonate, a sulfamoyl, a sulfonamido, a sulfonyl. It will beunderstood by those skilled in the art that the substituents canthemselves be substituted, if appropriate.

As used herein, the term “probe” means a compound of the invention whichis labeled with either a detectable label or an affinity tag, and whichis capable of binding, either covalently or non-covalently, to a proteinkinase domain. When, for example, the probe is non-covalently bound, itmay be displaced by a test compound. When, for example, the probe isbound covalently, it may be used to form cross-linked adducts, which maybe quantified and inhibited by a test compound.

The term “prodrug” denotes a compound that is a drug precursor which,upon administration to a subject, is converted within the body into acompound of Formula I, Formula IIa, Formula IIb or Formula IIc. Prodrugsof compounds of Formula I, Formula IIa, Formula IIb, Formula IIc orpharmaceutically acceptable salts or solvates thereof are within thescope of this disclosure.

The term “biologically active metabolite” means a pharmacologicallyactive product produced through metabolism in the body of a specifiedcompound or salt thereof.

The term “subject” or “patient” means a human or an animal subject forprevention or treatment.

In an embodiment the use is ex vivo, for example in vitro, such as an invitro assay.

The term “combination” within the meaning of this invention includes thesimultaneous, sequential or separate use of the components oringredients.

Compounds of the invention also include all isotopes of atoms present inthe Intermediates and/or final Compounds. Isotopes include those atomshaving the same atomic number but different mass numbers. For example,isotopes of hydrogen include deuterium and tritium.

Therapeutic Uses and Applications

The compounds of the present invention are inhibitors of protein kinaseactivity and are suitable for use in therapy.

An aspect of the present invention provides a method of inhibitingprotein kinase activity in a cell, the method comprising administeringto said cell compound of Formula I as defined herein, or apharmaceutically acceptable salt or solvate thereof.

In a further aspect, the present invention provides a method ofinhibiting protein kinase in vitro or in vivo, said method comprisingcontacting a cell with an effective amount of a compound of Formula I,Formula IIa, Formula IIb, Formula IIc or a pharmaceutically acceptablesalt, solvate, solvate of salt, stereoisomer, tautomer, isotope,prodrug, complex or biologically active metabolite thereof.

A further aspect of the present invention provides a method ofinhibiting protein kinase activity in a human or animal subject fortreatment or prevention of protein kinase mediated disease, the methodcomprising administering to said subject an effective amount of acompound of Formula I, Formula IIa, Formula IIb or Formula IIc asdefined herein, or a pharmaceutically acceptable salt or solvate ofsalt, stereoisomer, tautomer, isotope, prodrug, complex or biologicallyactive metabolite thereof.

The term “protein kinase mediated disease” is used herein associatedwith abnormal or undesirable cellular responses triggered or maintainedby protein kinase-mediated events. Furthermore, aberrant activation,mutation or excessive expressions of various protein kinases areimplicated in the mechanism of multiple diseases and disorders. Thesediseases include, but are not limited to cancer, autoimmune disease,inflammation, viral infection and neurological disease.

In one embodiment of this invention the disclosed compounds are used inthe treatment of a patient that suffers from a disease or disorder thatcan be treated by kinase inhibition. The compound disclosed hereinand/or pharmaceutically acceptable salt thereof can inhibit one or morekinases including but not limited to ITK, RLK (also known as TXK), BLK,BMX, BTK, JAK3, and/or TEC.

In one embodiment, the protein kinase inhibited by compounds of thepresent invention is ITK, BTK, BMX, RLK, or TEC singly or incombination.

The compounds of the present invention may be suitable for use in thetreatment of or prevention of diseases that involve ITK, BTK, BMX, RLKor TEC, i.e. diseases that involve T cells and/or NK cells, for example,cancer, autoimmune diseases, allergic diseases, inflammatory diseases,viral infection and combinations thereof.

In one embodiment, a compound disclosed herein and/or pharmaceuticallyacceptable salt thereof is administered to a patient in need orrecognized need thereof to prevent or treat an inflammatory disorder. Inanother embodiment, a compound disclosed herein and/or pharmaceuticallyacceptable salt thereof is administered to a patient in need orrecognized need thereof to prevent or treat an inflammatory disordercharacterized by excessive or undesired cytokine activity or production.In yet another embodiment, a compound and/or pharmaceutically acceptablesalt thereof is administered to a patient in need or recognized needthereof to prevent or treat lung inflammation, allergic asthma,pneumonia, psoriasis, atopic dermatitis or a combination thereof. In yetanother embodiment a compound and/or pharmaceutically acceptable saltthereof is administered to a patient in need of or recognized needthereof to prevent or treat uveitis or dry eye disease.

Examples of an autoimmune disease in the present invention includearthritis, systemic lupus erythematosus, rheumatoid arthritis,psoriasis, psoriatic arthritis, Still's disease, juvenile arthritis,type I diabetes, inflammatory bowel disease, myasthenia gravis,Hashimoto's thyroiditis, Ord's thyroiditis, Basedow's disease, Sjogren'ssyndrome, multiple sclerosis, Guillain-Barre syndrome, acutedisseminated encephalomyelitis, Addison disease, opsoclonus-myoclonussyndrome, ankylosing spondylitis, antiphospholipid antibody syndrome,aplastic anemia, autoimmune hepatitis, celiac disease, Goodpasture'ssyndrome, idiopathic thrombocytopenic purpura, optic neuritis,scleroderma, primary biliary cirrhosis, Reiter's disease, Takayasuarteritis, temporal arteritis, warm autoimmune hemolytic anemia, Wegenergranuloma, alopecia universalis, Burchett disease, chronic fatiguesyndrome, dysautonomia, endometriosis, interstitial cystitis, myotonia,vulvodynia, pemphigus, and combinations thereof.

Examples of an allergic disease in the present invention includeallergy, anaphylaxis, allergic conjunctivitis, allergic rhinitis, atopicdermatitis and the combinations thereof.

Examples of an inflammatory disease in the present invention includeasthma, appendicitis, blepharitis, bronchiolitis, bronchitis, bursitis,cervicitis, cholangitis, cholecystitis, colitis, conjunctivitis,cystitis, dacryoadenitis, dermatitis, dermatomyositis, encephalitis,endocarditis, endometritis, enteritis, epicondylitis, epididymitis,fasciitis, fibrositis, gastritis, gastroenteritis, hepatitis,hidradenitis suppurativa, inflammatory bowel disease, laryngitis,mastitis, meningitis, myelitis, myocarditis, myositis nephritis,oophoritis, orchitis, osteitis, osteoarthritis, pancreatitis, parotitis,pericarditis, peritonitis, pharyngitis, pleuritis, phlebitis, pneumonia,proctitis, prostatitis, pyelonephritis, rhinitis, salpingitis,sinusitis, stomatitis, synovitis, tendinitis, tonsillitis, uveitis,vaginitis, vasculitis, vulvitis, and combinations thereof.

Examples of a viral infection include HIV/AIDS, influenza andcombinations thereof.

Examples of cancer in the present invention include T-cell lymphomas andT-cell leukemias including peripheral T-cell lymphoma, Seazrysyndrome/cutaneous T-cell lymphoma, acute lymphoblastic leukemia, andadult T-cell leukemia/lymphoma. Additional examples include NK/T-celllymphoma, nasal type and aggressive NK-cell leukemia, as well asmelanoma and hepatocellular carcinoma.

In one embodiment, the compound of Formula I, Formula IIa, Formula IIb,Formula IIc or pharmaceutically acceptable salts, solvates, solvates ofsalts, stereoisomers, tautomers, isotopes, prodrugs, complexes, orbiologically active metabolites thereof, is acting by inhibiting one ormore of the host cell kinases involved in cell proliferation, cellsurvival, viral replication, autoimmunity, an inflammatory disease or aninfectious disease.

In further aspect of the present invention, is disclosed a method fortreating a subject suffering from a protein kinase mediated disease orcondition, comprising administering to the subject a therapeuticallyeffective amount of the compound of Formula I, Formula IIa, Formula IIb,Formula IIc, or pharmaceutically acceptable salt, solvate, solvate ofsalt, stereoisomer, tautomer, isotope, prodrug, complex or biologicallyactive metabolite thereof, in combination with at least onepharmaceutically acceptable carrier.

In further aspect of the present invention, the compound of Formula I,Formula IIa, Formula IIb, Formula IIc or pharmaceutically acceptablesalts, solvates, solvates of salts, stereoisomers, tautomers, isotopes,prodrugs, complexes, or biologically active metabolites thereof, isacting as inhibitor of cell kinases as anti-inflammatory, autoimmunemodulators or anti-cancer agents.

In a further aspect of the present invention, the compound of Formula I,Formula IIa, Formula IIb, Formula IIc or pharmaceutically acceptablesalts, solvates, solvates of salts, stereoisomers, tautomers, isotopes,prodrugs, complexes, or biologically active metabolites thereof, isacting by inhibiting one or more of the host cell kinases involved inT-cell function proliferation or polarization.

The compounds of Formula I, Formula IIa, Formula IIb, Formula IIc orpharmaceutically acceptable salts, solvates, solvates of salts,stereoisomers, tautomers, isotopes, prodrugs, complexes, or biologicallyactive metabolites thereof are suitable for use in the preparation of amedicament for inhibiting a protein kinase activity selected from ITK,BTK, BMX, RLK and combinations thereof in a subject.

The compounds of Formula I, Formula IIa, Formula IIb, Formula IIc orpharmaceutically acceptable salts, solvates, solvates of salts,stereoisomers, tautomers, isotopes, prodrugs, complexes, or biologicallyactive metabolites thereof and pharmaceutically acceptable compositionsof the present invention can be employed in combination therapies, thecompounds and pharmaceutically acceptable compositions may havepotential utility in combination with other therapies for the treatmentof cancer, viral infections, immune, inflammatory, neurologicaldiseases, proliferative and allergic disorders. Example includes but notlimited to co-administration with steroids, leukotriene antagonists,anti-histamines, anti-cancer, anti-viral, anti-biotic agents or otherprotein kinase inhibitors. The anti-cancer agent may be selected fromthe group consisting of: cell signal transduction inhibitors, mitosisinhibitors, alkylating agents, anti-metabolites, intercalatinganticancer agents, topoisomerase inhibitors, immunotherapic agents,anti-hormonal agents, and a mixture thereof. The additional activepharmaceutical ingredient used in the combination is appropriate for thedisease being treated and said additional active pharmaceuticalingredient is administered together with the compounds of Formula I,Formula IIa, Formula IIb, Formula IIc as a single dosage form orseparately as part of a multiple dosage form.

The compounds of the present invention are indicated both in thetherapeutic and/or prophylactic treatment of the above-mentionedconditions. For the above-mentioned therapeutic and/or prophylactic usesthe dosage administered will vary with the compound employed, thesubject, the mode of administration, the treatment desired and thedisorder indicated. The daily dosage may be between about 0.01 mg/kg toabout 100 mg/kg and preferably from about 1 mg/kg to about 25 mg/kg, ofthe subject body weight per day, one or more times a day, to obtain thedesired therapeutic effect.

A pharmaceutical acceptable composition of the present invention may beobtained by conventional procedures using conventional pharmaceuticalexcipients, well known in the art. It may typically comprisepharmaceutically acceptable additives, carriers or excipients. Thepharmaceutical composition of the present invention may be formulated inaccordance with conventional methods, and may be prepared in the form oforal formulations such as tablets, pills, powders, capsules, syrups,emulsions, microemulsions and others, or parenteral formulations such asintramuscular, intravenous or subcutaneous administrations.

For oral formulations, carriers or additives such as cellulose, calciumsilicate, corn starch, lactose, sucrose, dextrose, calcium phosphate,stearic acid, magnesium stearate, calcium stearate, gelatin, talc,surfactants, suspending agents, emulsifiers, diluents, and others may beused. Solid dosage forms for oral administration include capsules,tablets, pills, powders, and granules. Liquid dosage forms for oraladministration include, but are not limited to, pharmaceuticallyacceptable emulsions, microemulsions, solutions, suspensions, syrups andelixirs. The liquid dosage forms may contain inert diluents and can alsoinclude adjuvants such as wetting agents, emulsifying and suspendingagents, sweetening, flavoring, and perfuming agents.

The present invention contemplates compounds of Formula I, Formula IIa,Formula IIb, Formula IIc or pharmaceutical salts thereof. The inventionalso contemplates solvates, solvates of salts, stereoisomers, tautomers,isotopes, prodrugs, complexes or biologically active metabolites of thecompounds of Formula I, Formula IIa, Formula IIb and Formula IIc.

For Injectable formulations, sterile injectable aqueous or oleaginoussuspensions may be formulated according to the known art using suitabledispersing or wetting agents and suspending agents. The sterileinjectable preparation may also be a sterile injectable solution,suspension or emulsion in a nontoxic parenterally acceptable diluent orsolvent, for example, as a solution in 1,3-butanediol. Among theacceptable vehicles and solvents that may be employed are water,Ringer's solution, U.S.P. and isotonic sodium chloride solution. Inaddition, sterile, fixed oils are conventionally employed as a solventor suspending medium. For this purpose any bland fixed oil can beemployed including synthetic mono- or diglycerides. In addition, fattyacids such as oleic acid are used in the preparation of injectables.

The compounds of Formula I, Formula IIa, Formula IIb, Formula IIc, orpharmaceutically acceptable salt, solvate, solvate of salt,stereoisomer, tautomer, isotope, prodrug, complex, or biologicallyactive metabolites thereof and pharmaceutically acceptable compositionsof the present invention can be employed in combination therapies,wherein the additional active pharmaceutical ingredient is selected fromthe group comprising steroids, leukotriene antagonists, anti-histamines,anti-cancer, anti-viral, anti-biotic agents, protein kinase inhibitorsand combinations thereof.

A probe comprising the compound of Formula I, Formula IIa, Formula IIb,Formula IIc covalently conjugated to a detectable label or affinity tagfor said compound. The probe, wherein the detectable label is selectedfrom the group consisting of: a fluorescent moiety, a chemiluminescentmoiety, a paramagnetic contrast agent, a metal chelate, a radioactiveisotope containing moiety and biotin.

Specific Abbreviations Used

-   AIDS Acquired Immune Deficiency Syndrome-   ATP Adenosine Triphosphate-   BLK B lymphocyte kinase-   BMX Bone marrow-expressed kinase-   BTK Bruton's Tyrosine Kinase-   DMSO Dimethyl sulfoxide-   EDTA Ethylenediaminetetraacetic acid-   FCS Fetal Calf serum-   HIV Human immunodeficiency virus-   JAK3 Janus Kinase-   ITK Interleukin-2 inducible T-cell kinase-   NK/T-cell Natural killer T-cell-   PBMC Peripheral blood mononuclear cells-   PBS Phosphate buffered saline-   RPMI Roswell Park Memorial Institute medium-   RLK/TXK Resting lymphocyte kinase-   TEC Tyrosine kinase expressed in carcinoma-   Tec Family of protein-tyrosine kinases-   MS mass spectrometry-   ml milliliter-   μl microliter-   mmol millimole-   THF tetrahydrofuran-   DMF dimethylformamide-   MeOH methanol-   EtOH ethanol-   THF tetrahydrofuran-   DCM dichloromethane-   EtOAc Ethyl acetate-   AcOH acetic acid-   K₂CO₃ Potassium carbonate-   NaH Sodium hydride-   Pd/C Palladium on carbon-   TEA triethylamine-   DIPEA diisopropylethylamine-   DEA diethylamine-   NaHCO₃ sodium bicarbonate-   Cs₂CO₃ cesium carbonate-   NaBH(OAc)₃ sodium triacetoxyborohydride-   CbzCl benzyl chloroformate-   MsCl methanesulfonyl chloride-   Boc₂O di-tert-butyl dicarbonate-   MeI Iodomethane-   MgSO₄ magnesium sulfate-   Zn Zinc dust-   SO₃ Sulfur trioxide-   BrCN cyanogen bromide-   HBr hydrogen bromide-   HCl Hydrogen chloride-   TFA trifluoroacetic acid-   HATU    (1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium    3-oxide hexafluorophosphate)-   HBTU (2-(1H-benzotriazol-1-yl)-1,1,3,3-tetramethyluronium    hexafluorophosphate)-   Pd₂dba₃ Tris(dibenzylideneacetone)dipalladium(0)-   XPhos 2-Dicyclohexylphosphino-2′,4′,6′-triisopropyl biphenyl-   NaN₃ sodium azide

General Synthetic Methods

In the description of the synthetic methods described below and in thereferenced synthetic methods that are used to prepare the startingmaterials, it is to be understood that all proposed reaction conditions,including choice of solvent, reaction atmosphere, reaction temperature,duration of the experiment and workup procedures, can be selected by aperson skilled in the art.

The following section describes general synthetic method(s) which may beuseful in the preparation of compounds of the instant invention.

Compounds of Formula I where L-E is selected from

and X—Y is selected from —CH₂—NH—Y

are prepared as described below:

Intermediate A3 is obtained by reacting commercially availableIntermediate A1 with an amine of formula A2 where ring B₁, n and R¹ areas defined above and PG¹ is a suitable protecting group. Reductiveamination of Intermediate A3 with an amine of formula YNH₂ where Y is asdefined above provides Intermediate A4. Protection of the alkyl aminogroup with a suitable protective group PG² provides Intermediate A5.Reduction of the nitro group provides Intermediate A6 which is thencyclized to the corresponding aminobenzimidazole Intermediate A7.Coupling of Intermediate A7 with an acid of formula RCO₂H under standardcoupling conditions or with an activated acid of formula RC(O)LG, whereR is as defined above and LG is a leaving group, provides IntermediateA8. Removal of PG¹ protecting group provides Intermediate A9.

Compounds of Formula I are then obtained from Intermediate A9 by firstcoupling

Intermediate 9 with an acid of formula

under standard coupling conditions or with an activated acid of formula

where R^(a), R^(b) and Rc are as defined above and LG is a leaving groupfollowed by removal of PG² protective group.

Compounds of Formula I where L-E is selected from

and X—Y is selected from —CH₂—NH—Y are prepared in a similar manner bysubstituting

with

where ring B₂, n and PG¹ are as defined above.

Compounds of Formula I where L-E is selected from

and X—Y is selected from —CH₂—NR²—Y are prepared as described below:

Reduction of Intermediate A3 provides Intermediate B1. Protection of thealcohol group with a suitable protective group PG³ provides IntermediateB2. Reduction of the nitro group provides Intermediate B3 which is thencyclized to the corresponding aminobenzimidazole Intermediate B4.Coupling of Intermediate B4 with an acid of formula RCO₂H under standardcoupling conditions or with an activated acid of formula RC(O)LG where Ris as defined above and LG is a leaving group provides intermediateIntermediate B5. Removal of PG¹ and PG³ protecting groups providesintermediate Intermediate B6. Coupling of Intermediate B6 with an acidof formula

under standard coupling conditions or with an activated acid of formula

where R^(a), R^(b) and Rc are as defined above and LG is a leaving groupprovides Intermediate B7 which is oxidized to provide Intermediate B8.Reductive amination of Intermediate B8 with an amine of formula Y—NHR²where Y and R² are as described above provides compounds of Formula I.

Compounds of Formula I where L-E is selected from

and X—Y is —CH₂—NR²—Y are prepared in a similar manner by substituting

with

where ring B₂, n and PG¹ are as defined above.

Compounds of Formula I wherein L-E is selected from

and X—Y is selected from —C(O)NR²—Y are prepared as described below:

Intermediate C3 is obtained by coupling commercially availableIntermediate C1 with an amine of formula YNHR² where Y and R² are asdefined above under standard coupling conditions. Alternatively,Intermediate C3 is obtained in a 2 steps sequence by couplingIntermediate C1 with an amine of formula YNH₂ where Y is as definedabove under standard coupling conditions followed by reactingIntermediate C2 with an Intermediate of formula R²LG, where R² is asdefined above and LG is a leaving group, in a presence of a base.Intermediate C4 is obtained by reacting Intermediate C2 or C3 with anamine of formula A2 where ring B₁, n and R¹ are as defined above and PG¹is a suitable protecting group. Reduction of the nitro group providesIntermediate C5 which is then cyclized to the correspondingaminobenzimidazole Intermediate C6. Coupling of Intermediate C6 with anacid of formula RCO₂H under standard coupling conditions or with anactivated acid of formula RC(O)LG, where R is as defined above and LG isa leaving group, provides Intermediate C7. Removal of PG¹ protectinggroup provides Intermediate C8. Compounds of Formula I are then obtainedby coupling Intermediate C8 with an acid of formula

under standard coupling conditions or with an activated acid of formula

where Ra, R^(b) and Rc are as defined above and LG is a leaving group.

Compounds of Formula I where L-E is selected from

and X—Y is selected from —C(O)NR²—Y are prepared in a similar manner bysubstituting

with

where ring B₂, n and PG¹ are as defined above.

Compounds of Formula I where L-E is selected from

and X—Y is selected from —NR²C(O)—Y are prepared as described below:

Intermediate D3 is obtained in a 2 steps sequence by first reactingcommercially available Intermediate D1 with an acid of formula YCO₂Hunder standard coupling conditions or with an activated acid of formulaYC(O)LG, where Y is as defined above and LG is a leaving group, toprovide Intermediate D2; Intermediate D2 is then treated with R²LG,where R² is as defined above and LG is a leaving group, in a presence ofa base to provide Intermediate D3. Intermediate D4 is obtained byreacting Intermediate D2 or D3 with an amine of formula A2 where ringB₁, n and R¹ are as defined above and PG¹ is a suitable protectinggroup. Reduction of the nitro group provides Intermediate C5 which isthen cyclized to the corresponding aminobenzimidazole Intermediate D6.Coupling of Intermediate D6 with an acid of formula RCO₂H under standardcoupling conditions or with an activated acid of formula RC(O)LG where Ris as defined above and LG is a leaving group provides Intermediate D7.Removal of PG¹ protecting group provides Intermediate D8. Compounds ofFormula I are then obtained from Intermediate D8 by couplingIntermediate D8 with an acid of formula

under standard coupling conditions or with an activated acid of formula

where R^(a), R^(b) and Rc are as defined above and LG is a leavinggroup.

Compounds of Formula I where L is selected from

and X—Y is selected from —NR²C(O)—Y are prepared in a similar manner bysubstituting

with

where ring B₂, n and PG¹ are as defined above.

In an alternative method compounds of Formula I wherein L-E is selectedfrom

and X—Y is selected from —NR²C(O)—Y are prepared as described below:

Protection of commercially available Intermediate E1 providesIntermediate E2 where R² is as defined above and PG⁴ is a suitableprotecting group. Intermediate E3 is obtained by reacting IntermediatesE2 with an amine of formula A2 where ring B₁, n and R¹ are as definedabove and PG¹ is a suitable protecting group. Reduction of the nitrogroup provides Intermediate E4 which is then cyclized to thecorresponding aminobenzimidazole Intermediate E5. Coupling ofIntermediate E5 with an acid of formula RCO₂H under standard couplingconditions or with an activated acid of formula RC(O)LG where R is asdefined above and LG is a leaving group provides Intermediate E6.Removal of PG¹ protecting group provides Intermediate E7. IntermediatesE8 is obtained by coupling Intermediate E7 with an acid of formula

under standard coupling conditions or with an activated acid of formula

where R^(a), R^(b) and Rc are as defined above and LG is a leavinggroup. Removal of PG⁴ protecting group provides Intermediate E9.Coupling of Intermediate D9 with an acid of formula YCO₂H under standardcoupling conditions or with an activated acid of formula YC(O)LG where Yis as defined above and LG is a leaving group provides compounds ofFormula I.

Compounds of Formula I where L is selected from

and X—Y is selected from —NR²C(O)—Y are prepared in a similar manner bysubstituting

where ring B₂, n and PG¹ are as defined above.

Compounds of Formula I where L-E is selected from

and X—Y is selected from —NR²SO₂—Y are prepared as described below:

Intermediate F3 is obtained in a 2 steps sequence by first reactingcommercially available Intermediate F1 with an Intermediate of formulaY—SO₂-LG where Y is as defined and LG is a leaving group, followed byreacting Intermediate F2 with an Intermediate of formula R²LG, where R²is as defined above and LG is a leaving group, in a presence of a base.A Buchwald cross coupling reaction of Intermediates F2 or F3 with anamine of formula A2 provides Intermediate F4 where ring B₁, n and R¹ areas defined above and PG¹ is a suitable protecting group. Reduction ofthe nitro group provides Intermediate F5 which is then cyclized to thecorresponding aminobenzimidazole Intermediate F6. Coupling ofIntermediate F6 with an acid of formula RCO₂H under standard couplingconditions or with an activated acid of formula RC(O)LG where R is asdefined above and LG is a leaving group provides Intermediate F7.Removal of PG¹ protecting group provides Intermediate F8. Compounds ofFormula I are then obtained by coupling Intermediate F8 with an acid offormula

under standard coupling conditions or with an activated acid of formula

where R^(a), R^(b) and Rc are as defined above and LG is a leavinggroup.

Compounds of Formula I where L-E is selected from

and X—Y is selected from —NR²C(O)—Y are prepared in a similar manner bysubstituting

with

where ring B₂, n and PG¹ are as defined above.

Compounds of Formula I where L-E is selected from

and X—Y is selected from —O—CH₂—Y are prepared as described below:

Intermediate G2 is obtained by reacting commercially availableIntermediate G1 with an Intermediate of formula Y—CH₂-LG, where Y is asdescribed above and LG is a leaving group, in a presence of a base.Alternatively, Intermediate G2 is obtained by reacting Intermediate F1with an Intermediate of formula Y—CH₂—OH under Mitsunobu conditions. ABuchwald cross coupling reaction of Intermediate G2 with an amine offormula A2 provides Intermediate G3 where ring B₁, n and R¹ are asdefined above and PG¹ is a suitable protecting group. Reduction of thenitro group provides Intermediate G4 which is then cyclized to thecorresponding aminobenzimidazole Intermediate G5. Coupling ofIntermediate G5 with an acid of formula RCO₂H under standard couplingconditions or with an activated acid of formula RC(O)LG where R is asdefined above and LG is a leaving group provides Intermediate G6.Removal of PG¹ protecting group provides Intermediate G7. Compounds ofFormula I are obtained by coupling Intermediate G7 with an acid offormula

under standard coupling conditions or with an activated acid of formula

where R^(a), R^(b) and R^(c) are as defined above and LG is a leavinggroup.

Compounds of Formula I where L-E is selected from

and X—Y is selected from —O—CH₂—Y are prepared in a similar manner bysubstituting

with

where ring B₂, n and PG¹ are as defined above.

Compounds of Formula I wherein L-E is selected from

and X—Y is selected from —CH₂—NR³—Y are prepared as described below:

Compounds of Formula I where R³ is selected from —C(O)R⁴ as describedabove are obtained by reacting a compound of Formula I where X—Y isselected from —CH₂NH—Y with an acid of formula R⁴CO₂H under standardcoupling conditions or with an activated acid of formula R⁴C(O)LG whereR⁴ is as defined above and LG is a leaving group. Compounds of Formula Iwhere R³ is selected from —SO₂R⁴ as described above are obtained byreacting a compound of Formula I where X—Y is selected from —CH₂NH—Ywith an Intermediate of formula R⁴SO₂LG where R⁴ is as defined above andLG is a leaving group. Compounds of Formula I where R³ is selected from—C(O)OR⁴ as described above are obtained by reacting a compound ofFormula I where X—Y is selected from —CH₂NH—Y with an Intermediate offormula R⁴C(O)OLG where R⁴ is as defined above and LG is a leavinggroup.

Compounds of Formula I where L is selected from

and X—Y is selected from —CH₂—NR³—Y are prepared in a similar manner bysubstituting

with

where ring B₂, n and PG¹ are as defined above.

The following synthetic methods are intended to be representative of thechemistry used to prepare compound of Formula I of the present inventionand are not intended to be limiting.

Synthesis of Intermediate 1-h

Step 1: Intermediate 1-c

To a solution of 4-fluoro-3-nitrobenzaldehyde 1-a (812 mg, 4.8 mmol) andDIPEA (2.5 ml, 14.4 mmol) in acetonitrile was added dropwise a solutionof tert-butyl 3-aminophenylcarbamate 1-b (1.0 g, 4.8 mmol) inacetonitrile. After the addition was completed, the reaction was stirredovernight at room temperature. Volatiles were removed under reducedpressure. A saturated aqueous solution of ammonium chloride anddichloromethane were added to the residue, the organic layer wasseparated, and the aqueous phase was extracted twice withdichloromethane. The combined organic extracts were washed with brine,dried over MgSO₄, filtered and concentrated under reduced pressure.Purification by silica gel chromatography provided Intermediate 1-c as ayellow solid.

Step 2: Intermediate 1-e

To a solution of Intermediate 1-c (1.7 g, 4.7 mmol) and(S)-3,3-dimethylbutan-2-amine 1-e (481 mg, 4.7 mmol) in1,2-dichloroethane were sequentially added acetic acid (136 μl, 2.4mmol) and sodium triacetoxyborohydride (1.5 g, 7.1 mmol) and thereaction was stirred at room temperature overnight. A saturated aqueoussolution of NaHCO₃ and dichloromethane were then added, the organiclayer was separated, and the aqueous phase was extracted twice withdichloromethane. The combined organic extracts were washed with brine,dried over MgSO₄, filtered and concentrated under reduced pressure toprovide Intermediate 1-e as a yellow solid.

Step 3: Intermediate 1-f

To a solution of Intermediate 1-e (2.0 g, 4.5 mmol) in dichloromethanewere sequentially added sodium bicarbonate (380 mg) in water (9 ml) andbenzyl chloroformate (968 μl, 6.8 mmol) and the reaction was thenstirred for 2 hours at room temperature. A saturated aqueous solution ofammonium chloride and diethyl ether were added to the residue, theorganic layer was separated, and the aqueous phase was extracted twicewith diethyl ether. The combined organic extracts were washed withbrine, dried over MgSO₄, filtered and concentrated under reducedpressure. Purification by silica gel chromatography providedIntermediate 1-f as a beige oil.

Step 4: Intermediate 1-g

To a solution of Intermediate 1-f (1.5 g, 2.6 mmol) in MeOH (9.7 ml) wasadded a saturated aqueous solution of ammonium chloride (3.2 ml) andzinc dust (850 mg, 13.0 mmol) portionwise. The reaction was then stirredat 50° C. until completion, then cooled to room temperature and filteredover celite. The filtrate was concentrated under reduced pressure. Asaturated aqueous solution of NaHCO₃ and ethyl acetate were added to theresidue, the organic layer was separated, washed with brine, dried overMgSO₄, filtered and concentrated under reduced pressure to provideIntermediate 1-g as a purple solid.

Step 5: Intermediate 1-h

To a solution of Intermediate 1-g (1.3 g, 2.4 mmol) in EtOH (24.0 ml)was added cyanogen bromide (302 mg, 2.8 mmol) and the reaction wasstirred for 4 hours at room temperature. A saturated aqueous solution ofammonium chloride and ethyl acetate were then added, the organic layerwas separated, and the aqueous phase was extracted twice with ethylacetate. The combined organic extracts were washed with brine, driedover MgSO₄, filtered and concentrated under reduced pressure.Purification by silica gel chromatography provided Intermediate 1-h as apurple solid.

Synthesis of Intermediates 2-c

Step 1: Intermediate 2-b

To a solution of Intermediate 5-(difluoromethyl)thiophene-2-carboxylicacid 2-a (150 mg, 0.8 mmol) in DMF (3.5 ml) was added HATU (346 mg, 0.9mmol) and after stirring for 30 minutes a solution of Intermediate 1-h(400 mg, 0.7 mmol) and DIPEA (367 μl, 2.1 mmol) in DMF was addeddropwise. The reaction was then stirred at room temperature for 4 hours.A saturated aqueous solution of ammonium chloride and ethyl acetate werethen added, the organic layer was separated, washed with a saturatedaqueous solution of NaHCO₃ and brine, dried over MgSO₄, filtered andconcentrated under reduced pressure. Purification by silica gelchromatography provided Intermediate 2-b as a purple solid.

Step 2: Intermediate 2-c

To a solution of Intermediate 2-b (300 mg, 0.4 mmol) in dichloromethane(5 ml) was added TFA (2.5 ml, 32.7 mmol) at 0° C. and the solution wasstirred at room temperature until completion. Volatiles were removedunder reduced pressure to provide Intermediate 2-c.TFA as a white solid.

Synthesis of Compound 2

Step 1: Intermediate 3-a

To a solution of Intermediate 2-c.TFA (300 mg, 0.4 mmol) in THF (2 mL)cooled to −78° C. were sequentially added DIPEA (348 μl, 2.0 mmol) andacryloyl chloride (49 μL, 0.6 mmol) and the solution was stirred at −78°C. until completion. A saturated aqueous solution of ammonium chlorideand ethyl acetate were then added, the organic layer was separated, andthe aqueous phase was extracted twice with ethyl acetate. The combinedorganic extracts were washed with brine, dried over MgSO₄, filtered andconcentrated under reduced pressure to provide Intermediate 3-a as awhite foam.

Step 2: Compound 2

To a solution of Intermediate 3-a (250 mg, 0.3 mmol) in DCM (1 ml) wasadded a solution of 33% HBr in AcOH (990 μl, 5.4 mmol) at 0° C. and thesolution was then stirred at room temperature until completion. Diethylether was added and the precipitate was filtered off and washed twicewith diethyl ether. The solid was dissolved in THF and Cs₂CO₃ (500 mg)was added. The mixture was refluxed for 1 hour, then cooled to roomtemperature, filtered and concentrated under reduced pressure.Purification by silica gel chromatography provided Compound 2 as a whitesolid.

Compounds 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 19, 20, 24, 25, 26 and 82were prepared in a similar manner to Compound 2 by replacing5-(difluoromethyl)thiophene-2-carboxylic acid with 3-fluorobenzoic acid,3-methoxybenzoic acid, 3-cyanobenzoic acid, 4-chlorobenzoic acid,4-cyanobenzoic acid, thiazole-2-carboxylic acid, thiophene-2-carboxylicacid, 3-chlorobenzoic acid, isonicotinic acid, thiazole-5-carboxylicacid, nicotinic acid, 4-fluorobenzoic acid, 4-methoxy benzoic acid,5-(oxazol-5-yl)thiophene-2-carboxylic acid, 3-(benzyloxy)benzoic acidand 2-isopropylthiazole-5-carboxylic acid respectively.

Compounds 4, 5, 33 and 34 were prepared in a similar manner to Compound2 by replacing tert-butyl 3-aminophenylcarbamate 1-b with tert-butyl4-aminophenylcarbamate, tert-butyl 3-aminophenyl(methyl)carbamate,tert-butyl 3-amino-4-fluorophenylcarbamate and tert-butyl5-amino-2-fluorophenylcarbamate respectively,

Synthesis of Intermediate 4-f

Step 1: Intermediate 4-b

To a solution of 4-fluoro-3-nitrobenzaldehyde 1-a (1.5 g, 9.3 mmol) andDIPEA (4.9 ml, 28.0 mmol) in acetonitrile was added dropwise a solutionof Intermediate 4-a (2.0 g, 9.3 mmol) in acetonitrile. After theaddition was completed, the reaction was stirred overnight at roomtemperature. Volatiles were removed under reduced pressure. A saturatedaqueous solution of ammonium chloride and dichloromethane were added tothe residue, the organic layer was separated, and the aqueous phase wasextracted twice with dichloromethane. The combined organic extracts werewashed with brine, dried over MgSO₄, filtered and concentrated underreduced pressure. Purification by silica gel chromatography providedIntermediate 4-b as a yellow solid.

Step 2: Intermediate 4-c

To a solution of Intermediate 4-b (2.3 g, 6.3 mmol) and(S)-3,3-dimethylbutan-2-amine 1-d (640 mg, 6.3 mmol) in1,2-dichloroethane were sequentially added acetic acid (181 μl, 2.4mmol) and sodium triacetoxyborohydride (2.0 g, 9.5 mmol) and thereaction was stirred at room temperature overnight. A saturated aqueoussolution of NaHCO₃ and dichloromethane were then added, the organiclayer was separated, and the aqueous phase was extracted twice withdichloromethane. The combined organic extracts were washed with brine,dried over MgSO₄, filtered and concentrated under reduced pressure toprovide Intermediate 4-c as an orange solid.

Step 3: Intermediate 4-d

To a solution of Intermediate 4-c (2.2 g, 5.0 mmol) in dichloromethanewere sequentially added sodium bicarbonate (420 mg) in water (10 ml) andbenzyl chloroformate (1.0 ml, 7.5 mmol) and the reaction was thenstirred overnight at room temperature. Volatiles were removed underreduced pressure. A saturated aqueous solution of ammonium chloride andethyl acetate were added to the residue, the organic layer wasseparated, and the aqueous phase was extracted twice with ethyl acetate.The combined organic extracts were washed with brine, dried over MgSO₄,filtered and concentrated under reduced pressure. Purification by silicagel chromatography provided Intermediate 4-d as a beige oil.

Step 4: Intermediate 4-e

To a solution of Intermediate 4-d (1.7 g, 2.9 mmol) in MeOH (9.7 ml) wasadded a saturated aqueous solution of ammonium chloride (4.8 ml) andzinc dust (954 mg, 13.0 mmol) portion wise. The reaction was thenstirred at 50° C. until completion, then cooled to room temperature andfiltered over celite. The filtrate was concentrated under reducedpressure. A saturated aqueous solution of NaHCO₃ and ethyl acetate wereadded to the residue, the organic layer was separated, washed withbrine, dried over MgSO₄, filtered and concentrated under reducedpressure. Diethyl ether was added to the residue; a precipitate formedand was collected by filtration to provide Intermediate 4-e as a purplesolid.

Step 5: Intermediate 4-f

To a solution of Intermediate 4-e (1.5 g, 2.7 mmol) in EtOH (24 ml) wasadded cyanogen bromide (345 mg, 3.2 mmol) and the reaction was stirredfor 4 hours at room temperature. A saturated aqueous solution ofammonium chloride and ethyl acetate were then added, the organic layerwas separated, and the aqueous phase was extracted twice with ethylacetate. The combined organic extracts were washed with brine, driedover MgSO₄, filtered and concentrated under reduced pressure. Diethylether was added to the residue; a precipitate formed and was collectedby filtration to provide Intermediate 4-f as a purple solid.

Synthesis of Intermediate 5-b

Step 1: Intermediate 5-a

To a solution of 5-(difluoromethyl)thiophene-2-carboxylic acid 2-a (351mg, 0.6 mmol) in DMF (3.0 ml) cooled to 0° C. was added HATU (301 mg,0.8 mmol) and after stirring for 30 minutes a solution of Intermediate4-f (130 mg, 0.7 mmol) and DIPEA (319 μl, 2.1 mmol) in DMF was addeddropwise. The reaction was then stirred at room temperature for 4 hours.A saturated aqueous solution of ammonium chloride and ethyl acetate werethen added, the organic layer was separated, washed with a saturatedaqueous solution of NaHCO₃ and brine, dried over MgSO₄, filtered andconcentrated under reduced pressure. Purification by silica gelchromatography provided Intermediate 5-a as a purple solid.

Step 2: Intermediate 5-b

To a solution of Intermediate 5-a (300 mg, 0.4 mmol) in dichloromethane(5 ml) was added TFA (2.5 ml, 32.7 mmol) at 0° C. and the solution wasstirred at room temperature until completion. Volatiles were removedunder reduced pressure to provide Intermediate 5-b.TFA as an off-whitesolid.

Synthesis of Compound 3

Step 1: Intermediate 6-a

To a solution of Intermediate 5-b.TFA (310 mg, 0.4 mmol) in THF (2 mL)cooled to −78° C. were sequentially added DIPEA (700 μl, 4.1 mmol) and3-bromopropanoyl chloride (62 μL, 0.6 mmol) and the solution was stirredat −78° C. until completion. A saturated aqueous solution of ammoniumchloride and ethyl acetate were then added, the organic layer wasseparated, and the aqueous phase was extracted twice with ethyl acetate.The combined organic extracts were washed with brine, dried over MgSO₄,filtered and concentrated under reduced pressure to provide Intermediate6-a as a white foam.

Step 2: Intermediate 6-b

To a solution of Intermediate 6-a (320 mg, 0.4 mmol) in dichloromethane(1.5 ml) was added a solution of 33% HBr in AcOH (1.1 ml, 6.2 mmol) at0° C. and the solution was then stirred at room temperature untilcompletion. Diethyl ether was added; a precipitate formed and wascollected by filtration, washed twice with diethyl ether and dried undervacuum to provide Intermediate 6-b as a white solid.

Step 3: Compound 3

To a solution of Intermediate 6-b (260 mg, 0.4 mmol) in THF was addedDIPEA (1.0 ml, 5.7 mmol) and the reaction was stirred at roomtemperature overnight. Volatiles were removed under reduced pressure.Purification by silica gel chromatography provided Compound 3 as a whitesolid.

Compounds 54, 55, 67 and 71 were prepared in a similar manner toCompound 3 by replacing 5-(difluoromethyl)thiophene-2-carboxylic acidwith 4-cyanobenzoic acid, nicotinic acid, isothiazole-5-carboxylic acidand 5-(oxazol-5-yl)thiophene-2-carboxylic acid respectively.

Compounds 1, 6, 18, 58, 62, 68 and 81 were prepared in a similar mannerto Compound 3 by replacing

respectively for the synthesis Intermediate 4-f.

Synthesis of Intermediate 7-d

Step 1: Intermediate 7-a

To a solution of Intermediate 1-c (5.0 g, 14.0 mmol) in ethanol (200 ml)was added portion wise sodium borohydride (794 mg, 21.0 mmol) and thereaction was stirred at room temperature for 1 hour. A saturated aqueoussolution of NaHCO₃ was slowly added and after stirring for 15 minutesvolatiles were removed under reduced pressure. Ethyl acetate was added,the organic layer was separated, washed with a saturated aqueoussolution of NaHCO₃ and brine, dried over MgSO₄, filtered andconcentrated under reduced pressure to provide Intermediate 7-a as abeige foam.

Step 2: Intermediate 7-b

To a solution of Intermediate 7-a (5.0 g, 13.9 mmol) in dichloromethane(143 ml) cooled to 0° C. were sequentially added imidazole (1.9 g, 29.2mmol) and tert-butylchlorodimethylsilane (2.2 g, 14.6 mmol) portionwise. The reaction was then warmed to room temperature and stirredovernight. A saturated aqueous solution of ammonium chloride and ethylacetate were added, the organic layer was separated, washed with asaturated aqueous solution of ammonium chloride and brine, dried overMgSO₄, filtered and concentrated under reduced pressure to provideIntermediate 7-b as a beige oil.

Step 3: Intermediate 7-c

To a solution of Intermediate 7-b (5.0 g, 10.6 mmol) in methanol andstirred under nitrogen was added 10% Pd/C (225 mg, 1.1 mmol). Thereaction mixture was purged with H₂ and stirred for 24 hours under H₂.The reaction was then filtered through celite and the filtrate wasconcentrated under reduced pressure to provide Intermediate 7-c as abeige solid.

Step 4: Intermediate 7-d

To a solution of Intermediate 7-c (4.5 g, 10.1 mmol) in EtOH (51 ml) wasadded cyanogen bromide (1.3 g, 12.2 mmol) and the reaction was stirredfor 2 hours at room temperature. Volatiles were removed under reducedpressure. A saturated aqueous solution of ammonium chloride and ethylacetate were then added to the residue, the organic layer was separated,washed with a saturated aqueous solution of NaHCO₃ and brine, dried overMgSO₄, filtered and concentrated under reduced pressure to provideIntermediate 7-d as a beige foam.

Synthesis of Compound 85

Step 1: Intermediate 8-a

To a solution of 5-(difluoromethyl)thiophene-2-carboxylic acid 2-a (1.2g, 7.1 mmol) in DMF (32.0 ml) cooled to 0° C. was added HATU (3.2 g, 8.3mmol) and after stirring for 30 minutes a solution of Intermediate 7-d(3.0 mg, 6.4 mmol) and DIPEA (3.3 ml, 19.2 mmol) in DMF was addeddropwise. The reaction was then stirred at room temperature overnight. Asaturated aqueous solution of ammonium chloride and ethyl acetate werethen added, the organic layer was separated, washed with a saturatedaqueous solution of NaHCO₃ and brine, dried over MgSO₄, filtered andconcentrated under reduced pressure. Purification by silica gelchromatography provided Intermediate 8-a as a purple solid.

Step 2: Intermediate 8-b

To a solution of Intermediate 8-a (2.5 g, 3.9 mmol) in MeOH (5 ml) wasadded 4N HCl in 1,4-dioxane (50.0 ml, 1646.0 mmol) and the solution wasstirred at room temperature overnight. Volatiles were removed underreduced pressure and diethyl ether was added to the residue. Aprecipitate formed and was collected by filtration, dried under vacuumto provide Intermediate 8-b.HCl as a purple solid.

Step 3: Intermediate 8-c

To a solution of Intermediate 8-b.HCl (77 mg, 0.2 mmol) intetrahydrofuran (1.8 ml) cooled to −78° C. were sequentially added DIPEA(323 μl, 1.8 mmol) and acryloyl chloride (15 μl, 0.2 mmol) and thereaction was stirred at −78° C. for 2 hours. Water (20 mL) and ethylacetate (20 mL) were added, the organic layer was separated, washed witha saturated aqueous solution of NaHCO₃ and brine, dried over anhydrousMgSO₄, filtered and concentrated under reduced pressure to provideIntermediate 8-c as a beige solid.

Step 4: Compound 85

To a solution of Intermediate 8-c (1.8 g, 3.8 mmol) in THF (15 ml) andDMSO (10.0 ml) cooled to 0° C. were sequentially added DIPEA (2.7 ml,15.4 mmol) and a solution of SO₃ pyridine complex (1.8 g, 11.5 mmol) inDMSO (5 mL). The mixture was stirred at 0° C. until completion.Volatiles were removed under reduced pressure, water was added, aprecipitate formed and was collected by filtration, washed with waterand dried under vacuum to provide Intermediate 8-d as a beige solid.

Synthesis of Compound 14

To a solution of Compound 85 (40 mg, 0.09 mmol) and cyclohexylamine(10.0 μl, 0.09 mmol) in dichloroethane (700 μl) and THF (70 μl) weresequentially added acetic acid (2 μl, 0.04 mmol) and sodiumtriacetoxyborohydride (27 mg, 0.13 mmol) and the reaction was stirred atroom temperature overnight. Volatiles were removed under reducedpressure. Purification by silica gel chromatography provided Compound 14as a white solid.

Compounds 21, 22, 23, 29, 30, 31, 35, 39, 40, 46, 47, 59 and 66 wereprepared in a similar manner to Compound 14 by replacing cyclohexylaminewith (S)-butan-2-amine, (R)-2-amino-3,3-dimethylbutan-1-ol,2,2-dimethylpropan-1-amine, 3-amino-2,2-dimethylpropan-1-ol,(R)-3,3-dimethylbutan-2-amine, trans 4-aminocyclohexanol, cis4-aminocyclohexanol, 3-aminopropan-1-ol, ethanamine,2-(2-methoxyethoxy)ethanamine, (S)-2-amino-3,3-dimethylbutan-1-ol,2-(piperazin-1-yl)ethanol and N-(3-(2-(3-aminopropoxy)ethoxy)propyl)acetamide respectively.

Synthesis of Compound 32

To a solution of Compound 85 (40 mg, 0.09 mmol) and pyrrolidine (6.1 mg,0.09 mmol) in THF (2.0 ml) was added acetic acid (2 μl, 0.04 mmol) andsodium triacetoxyborohydride (27 mg, 0.13 mmol) and the reaction wasstirred at room temperature overnight. Volatiles were removed underreduced pressure. Purification by silica gel chromatography providedCompound 32 as a white solid.

Compounds 44, 45, 50 and 61 were prepared in a similar manner toCompound 32 by replacing pyrrolidine with (R)-pyrrolidin-2-ylmethanol,(S)-pyrrolidin-2-ylmethanol, morpholine and(2S,6R)-2,6-dimethylmorpholine respectively.

Synthesis of Intermediate 10-d

Step 1: Intermediate 10-b

To a solution of trans 4-aminocyclohexanol 10-a (1 g, 8.7 mmol) inacetonitrile (43.4 ml) were sequentially added potassium carbonate (6.0g, 43.4 mmol) and benzyl bromide (2.06 ml, 17.4 mmol) dropwise. Thereaction was stirred at room temperature overnight and then filtered.Volatiles were removed under reduced pressure to provide Intermediate10-b as a beige oil.

Step 2: Intermediate 10-c

To a solution of Intermediate 10-b (2.5 g, 8.5 mmol) and1-bromo-2-methoxyethane (3.5 g, 25.4 mmol) in DMPU (8.5 ml) was slowlyadded NaH (60% dispersion in mineral oil, 846 mg, 21.2 mmol), and thereaction was then stirred at room temperature for 18 hours. Water andethyl acetate were added; the organic layer was separated, washed with asaturated aqueous solution of NaHCO₃ and brine, dried over anhydrousMgSO₄, filtered and concentrated under reduced pressure. Purification bysilica gel chromatography provided Intermediate 10-c as beige oil.

Step 3: Intermediate 10-d

To a solution of Intermediate 10-c (2.5 g, 7.1 mmol) in methanol andstirred under nitrogen was added 10% Pd/C (200 mg, 0.9 mmol). Thereaction mixture was purged with H₂ and stirred for 1 day under 60 psiof H₂. The reaction was then filtered through celite and the filtratewas concentrated under reduced pressure to provide Intermediate 10-d asa white foam.

Synthesis of Compound 51

To a solution of Compound 85 (50 mg, 0.11 mmol) and Intermediate 10-d(28 mg, 0.16 mmol) in THF (1 ml) and acetonitrile (1 ml) was addedsodium triacetoxyborohydride (34 mg, 0.16 mmol) and the reaction wasstirred at room temperature overnight. Volatiles were removed underreduced pressure. Purification by silica gel chromatography providedCompound 51 as a white solid.

Compounds 52 and 60 were prepared in a similar manner to Compound 51 byreplacing trans 4-aminocyclohexanol with(R)-2-amino-3,3-dimethylbutan-1-ol and cis 4-aminocyclohexanolrespectively for the synthesis of Intermediate 10-d.

Synthesis of Compound 41

Step 1: Intermediate 12-a

To a solution of pyrimidine-5-carboxylic acid (53 mg, 0.4 mmol) in DMFcooled to 0° C. was added HATU (211 mg, 0.5 mmol) and after stirring for30 minutes a solution of Intermediate 7-d (200 mg, 0.4 mmol) and DIPEA(224 μl, 1.3 mmol) in DMF was added dropwise. The reaction was thenstirred at room temperature for 3 days. A saturated aqueous solution ofammonium chloride and ethyl acetate were then added, the organic layerwas separated, washed with a saturated aqueous solution of NaHCO₃ andbrine, dried over anhydrous MgSO₄, filtered and concentrated underreduced pressure. Purification by silica gel chromatography providedIntermediate 12-a as a purple solid.

Step 2: Intermediate 12-b

To a solution of Intermediate 12-a (54 mg, 0.09 mmol) in MeOH (2 ml) wasadded 4N HCl in dioxane (5 ml, 30 mmol) and the solution was stirred atroom temperature overnight. Volatiles were removed under reducedpressure to provide Intermediate 12-b as a beige solid.

Step 3: Intermediate 12-c

To a solution of Intermediate 12-b.HCl (34 mg, 0.09 mmol) in THF (2 mL)and NMP (1 ml) cooled to −78° C. were sequentially added DIPEA (163 μl,0.94 mmol) and acryloyl chloride (8 μL, 0.09 mmol) and the solution wasstirred at −78° C. until completion. Volatiles were removed underreduced pressure, water was added to the residue, a precipitate formedand was collected by filtration, washed with water and dried undervacuum to provide Intermediate 12-c as a beige solid.

Step 4: Compound 86

To a solution of Intermediate 12-c (40 mg, 0.09 mmol) in THF (1.5 ml)and DMSO (1.5 ml) cooled to 0° C. were sequentially added DIPEA (67 μl,0.38 mmol) and a solution of SO₃ pyridine complex (46 mg, 0.29 mmol) inDMSO (1 mL). The mixture was then stirred at room temperature overnight.Volatiles were removed under reduced pressure, water was added, aprecipitate formed and was collected by filtration, washed with waterand dried under vacuum to provide Compound 86 as a beige solid.

Step 5: Compound 41

To a solution of Compound 86 (40 mg, 0.09 mmol) and(S)-3,3-dimethylbutan-2-amine 1-d (18 μl, 0.14 mmol) in MeOH (2 ml) anddichloromethane (500 μl) were sequentially added acetic acid (2.8 μl,0.048 mmol) and sodium triacetoxyborohydride (31 mg, 0.14 mmol) and thereaction was stirred at room temperature overnight. Volatiles wereremoved under reduced pressure. Purification by silica gelchromatography provided Compound 41 as a white solid.

Compounds 27, 28, 37, 38, 42, 43 and 49 were prepared in a similarmanner to Compound 41 by replacing pyrimidine-5-carboxylic acid withpicolinic acid, 1-methyl-1H-pyrazole-5-carboxylic acid,4-(benzyloxy)benzoic acid, isoxazole-5-carboxylic acid,oxazole-5-carboxylic acid, isothiazole-5-carboxylic acid and1-methyl-1H-pyrazole-4-carboxylic acid respectively.

Synthesis of Compound 87

Step 1: Intermediate 13-a

To a solution of isoxazole-5-carboxylic acid (330 mg, 2.9 mmol) in DMF(24 ml) cooled to 0° C. was added HATU (1.2 g, 3.2 mmol) and afterstirring for 30 minutes a solution of Intermediate 7-d (1.1 g, 2.4 mmol)and DIPEA (1.3 ml, 7.3 mmol) in DMF (3 ml) was added dropwise. Thereaction was then stirred at room temperature for 1 day. A saturatedaqueous solution of ammonium chloride and ethyl acetate were then added,the organic layer was separated, washed with a saturated aqueoussolution of NaHCO₃ and brine, dried over anhydrous MgSO₄, filtered andconcentrated under reduced pressure. Purification by silica gelchromatography provided Intermediate 13-a as a beige solid.

Step 2: Intermediate 13-b

To a solution of Intermediate 13-a (1.1 g, 2.0 mmol) in MeOH (1 ml) wasadded 4N HCl in dioxane (10.0 ml, 40.0 mmol) and the solution wasstirred at room temperature overnight. Volatiles were removed underreduced pressure to provide Intermediate 13-b.HCl as a beige solid.

Step 3: Intermediate 13-c

To a solution of Intermediate 13-b.HCl (700 mg, 2.0 mmol) in THF (20.0mL) and NMP (1.5 ml) cooled to −78° C. were sequentially added DIPEA(3.5 ml, 20.0 mmol) and acryloyl chloride (163 μL, 2.0 mmol) and thesolution was stirred at −78° C. for 30 minutes. Volatiles were removedunder reduced pressure, water was added to the residue, a precipitateformed and was collected by filtration, washed with water and driedunder vacuum to provide Intermediate 13-c as a beige solid.

Step 4: Compound 87

To a solution of Intermediate 13-c (620 mg, 1.5 mmol) in THF (3.1 ml)and DMSO (1.1 ml) cooled to 0° C. were sequentially added DIPEA (1.1 ml,6.1 mmol) and a solution of SO₃ pyridine complex (734 mg, 4.6 mmol) inDMSO (10.0 mL). The mixture was then stirred at 0° C. for 2 hours.Volatiles were removed under reduced pressure, water was added, aprecipitate formed and was collected by filtration, washed with waterand dried under vacuum to provide Compound 87 as a beige solid.

Synthesis of Compound 76

To a solution of Compound 87 (150 mg, 0.4 mmol) and morpholine (36 μl,0.4 mmol) in dichloroethane (2.0 ml), were sequentially added aceticacid (11 μl, 0.2 mmol) and sodium triacetoxyborohydride (792 mg, 3.7mmol) and the reaction was stirred overnight at room temperature.Volatiles were removed under reduced pressure. Purification by silicagel chromatography provided Compound 76 as a white solid.

Compounds 74 was prepared in a similar manner to Compound 76 byreplacing morpholine with trans-4-aminocyclohexanol

Synthesis of Compound 88

Step 1: Intermediate 15-a

To a solution of isothiazole-5-carboxylic acid (331 mg, 2.6 mmol) in DMF(21 ml) cooled to 0° C. was added HATU (1.0 g, 2.8 mmol) and afterstirring for 30 minutes a solution of Intermediate 7-d (1.0 g, 2.1 mmol)and DIPEA (1.1 ml, 6.4 mmol) in DMF (3 ml) was added dropwise. Thereaction was then stirred at room temperature for 1 day. A saturatedaqueous solution of ammonium chloride and ethyl acetate were then added,the organic layer was separated, washed with a saturated aqueoussolution of NaHCO₃ and brine, dried over anhydrous MgSO₄, filtered andconcentrated under reduced pressure. Purification by silica gelchromatography provided Intermediate 15-a as a beige solid.

Step 2: Intermediate 15-b

To a solution of Intermediate 15-a (950 mg, 1.6 mmol) in MeOH (1 ml) wasadded 4N HCl in dioxane (10.0 ml, 40.0 mmol) and the solution wasstirred at room temperature overnight. Volatiles were removed underreduced pressure, diethyl ether and hexanes were added to the residue, aprecipitate formed and was collected by filtration, dried under vacuumto provide Intermediate 15-b.HCl as a beige solid.

Step 3: Intermediate 15-c

To a solution of Intermediate 15-b. HCl (600 mg, 1.6 mmol) in THF (26.0mL) and NMP (1.5 ml) cooled to −78° C. were sequentially added DIPEA(2.9 ml, 16.4 mmol) and acryloyl chloride (133 μL, 1.6 mmol) and thesolution was stirred at −78° C. for 30 minutes. Volatiles were removedunder reduced pressure, water was added to the residue, a precipitateformed and was collected by filtration, washed with water and driedunder vacuum to provide Intermediate 15-c as a beige solid.

Step 4: Compound 88

To a solution of Intermediate 15-c (500 mg, 1.2 mmol) in THF (5.6 ml)and DMSO (2.0 ml) cooled to 0° C. were sequentially added DIPEA (2.0 ml,11.2 mmol) and a solution of SO₃ pyridine complex (1.4 g, 8.4 mmol) inDMSO (1.0 mL). The mixture was then stirred at 0° C. for 1 hour.Volatiles were removed under reduced pressure, water was added, aprecipitate formed and was collected by filtration, washed with waterand dried under vacuum to provide Compound 88 as a beige solid.

Synthesis of Compound 75

To a solution of Compound 88 (150 mg, 0.4 mmol) andtrans-4-aminocyclohexanol (43 mg, 0.4 mmol) in tetrahydrofuran (2.0 ml),were sequentially added acetic acid (10 μl, 0.2 mmol) and sodiumtriacetoxyborohydride (114 mg, 0.5 mmol) and the reaction was stirredovernight at room temperature. Volatiles were removed under reducedpressure. Purification by silica gel chromatography provided compound 75as a white solid.

Compound 73 was prepared in a similar manner to Compound 75 by replacingtrans-4-aminocyclohexanol with morpholine.

Synthesis of Intermediate 17-f

Step 1: Intermediate 17-b

To a solution of 4-fluoro-3-nitrobenzaldehyde 1-a (722 mg, 4.3 mmol) andDIPEA (2.2 ml, 12.8 mmol) in acetonitrile was added dropwise a solutionof Intermediate 17-a (1.0 g, 4.3 mmol) in acetonitrile. After theaddition was completed, the reaction was stirred overnight at roomtemperature. Volatiles were removed under reduced pressure. A saturatedaqueous solution of ammonium chloride and ethyl acetate were added tothe residue, the organic layer was separated, washed with brine, driedover MgSO₄, filtered and concentrated under reduced pressure to provideIntermediate 17-b as an orange foam.

Step 2: Intermediate 17-c

To a solution of Intermediate 17-b (1.6 g, 4.2 mmol) and(S)-3,3-dimethylbutan-2-amine 1-d (625 μl, 4.6 mmol) in dichloromethane(35.0 ml), were sequentially added acetic acid (119 μl, 2.1 mmol) andsodium triacetoxyborohydride (1.3 g, 6.3 mmol) and the reaction wasstirred overnight at room temperature. A saturated aqueous solution ofNaHCO₃ and dichloromethane were added, the organic layer was separated,washed with brine, dried over anhydrous MgSO₄, filtered and concentratedunder reduced pressure. Purification by silica gel chromatographyprovided Intermediate 17-c as a beige solid.

Step 3: Intermediate 17-d

To a solution of Intermediate 17-c (1.9 g, 4.0 mmol) in dichloromethane(15 ml) were sequentially added sodium bicarbonate (341 mg) in water (20ml) and benzyl chloroformate (868 μl, 6.1 mmol) and the reaction wasthen stirred overnight at room temperature. A saturated aqueous solutionof ammonium chloride and dichloromethane were added to the residue, theorganic layer was separated, washed with brine, dried over anhydrousMgSO₄, filtered and concentrated under reduced pressure to provideIntermediate 17-d as an orange oil.

Step 4: Intermediate 17-e

To a solution of Intermediate 17-d (2.4 g, 4.0 mmol) in MeOH (26.0 ml)was added a saturated aqueous solution of ammonium chloride (15.0 ml)and zinc dust (1.3 g, 19.9 mmol) portion wise. The reaction was thenstirred at 50° C. for 1 hour, then cooled to room temperature andfiltered over celite. The filtrate was concentrated under reducedpressure. Diethyl ether and a saturated aqueous solution of NaHCO₃ wereadded to the residue, the organic layer was separated, washed withbrine, dried over MgSO₄, filtered and concentrated under reducedpressure to provide Intermediate 17-e as a beige solid.

Step 5: Intermediate 17-f

To a solution of Intermediate 17-e (2.3 g, 4.0 mmol) in EtOH (20.0 ml)was added cyanogen bromide (510 mg, 4.8 mmol) and the reaction wasstirred for 4 hours at room temperature. Volatiles were removed underreduced pressure. A saturated aqueous solution of ammonium chloride andethyl acetate were then added to the residue, the organic layer wasseparated, washed with a saturated aqueous solution of NaHCO₃ and brine,dried over MgSO₄, filtered and concentrated under reduced pressure toprovide Intermediate 17-f as a beige solid.

Synthesis of Intermediate 18-a

Step 1: Intermediate 18-a

To a solution of 5-(difluoromethyl)thiophene-2-carboxylic acid 2-a (137mg, 0.8 mmol) in DMF (3.2 ml) cooled to 0° C. was added HATU (317 mg,0.8 mmol) and after stirring for 30 minutes a solution of Intermediate17-f (383 mg, 0.6 mmol) and DIPEA (336 μl, 1.9 mmol) in DMF (1.2 ml) wasadded dropwise. The reaction was then stirred at room temperature for 1day. A saturated aqueous solution of ammonium chloride and ethyl acetatewere then added, the organic layer was separated, washed with asaturated aqueous solution of ammonium chloride and brine, dried overanhydrous MgSO₄, filtered and concentrated under reduced pressure.Purification by silica gel chromatography provided Intermediate 18-a asa yellow solid.

Step 2: Intermediate 18-b

To a solution of Intermediate 18-a (177 mg, 0.2 mmol) in MeOH (1 m11)was added 4N HCl in dioxane (4.0 ml, 16.0 mmol) at room temperature andthe solution was stirred for 1 hour. Volatiles were removed underreduced pressure, diethyl ether was added, a precipitate formed and wascollected by filtration, dried under vacuum to provide Intermediate18-b.HCl as a white solid.

Synthesis of Compound 56

Step 1: Intermediate 19-a

To a solution of Intermediate 18-b.HCl (138 mg, 0.2 mmol) in THF (20.0mL) cooled to −78° C. were sequentially added TEA (277 μl, 1.2 mmol) andacryloyl chloride (24 μL, 0.3 mmol) and the solution was stirred at −78°C. for 30 minutes. A saturated aqueous solution of ammonium chloride andethyl acetate were then added, the organic layer was separated, and theaqueous phase was extracted twice with ethyl acetate. The combinedorganic extracts were washed with brine, dried over MgSO₄, filtered andconcentrated under reduced pressure to provide Intermediate 19-a as anoff white foam.

Step 2: Intermediate 19-b

To a solution of Intermediate 19-a (130 mg, 0.2 mmol) in dichloromethane(2.0 ml) was added a solution of 33% HBr in AcOH (2.0 ml, 12.1 mmol) at0° C. and the solution was then stirred at room temperature untilcompletion. Diethyl ether was added; a precipitate formed and wascollected by filtration then dried under vacuum to provide Intermediate19-b as a white solid.

Step 3: Compound 56

To a solution of Intermediate 19-b (120 mg, 0.2 mmol) in THF was addedcesium carbonate (475 mg, 1.5 mmol) and the reaction was heated at 60°C. overnight then cooled to room temperature and filtered. The filtratewas concentrated under reduced pressure. Purification by silica gelchromatography provided Compound 56 as a white solid.

Compounds 57 was prepared in a similar manner to compound 56 byreplacing tert-butyl 6-aminoindoline-1-carboxylate with tert-butyl6-amino-2H-benzo[b][1,4]oxazine-4(3H)-carboxylate for the synthesis ofIntermediate 17-f.

Synthesis of Intermediate 20-e

Step 1: Intermediate 20-b

To a solution of 3-aminocyclobutanol HCl H₂O 20-a (25.0 g, 177.0 mmol)in EtOH (88 ml) were sequentially added TEA (88.0 ml) and Boc₂O (53.3ml, 230.0 mmol) and the mixture was stirred at room temperatureovernight. Volatiles were removed under reduced pressure. Water andethyl acetate were added to the residue, the organic layer wasseparated, washed with a saturated aqueous solution of ammoniumchloride, 10% aqueous citric acid, a saturated aqueous solution ofNaHCO₃ and brine, dried over anhydrous MgSO₄, filtered and concentratedunder reduced pressure to provide Intermediate 20-b as a white solid.

Step 2: Intermediate 20-c

To a solution of Intermediate 20-b (2.0 g, 10.7 mmol) in dichloromethane(42.7 ml) were sequentially added TEA (3.0 ml, 21.4 mmol) andmethanesulfonyl chloride (1.3 ml, 16.0 mmol) at 0° C. and the reactionwas then stirred at room temperature for 1 hour. A saturated aqueoussolution of ammonium chloride was added, the organic layer wasseparated, washed with brine, dried over anhydrous MgSO₄, filtered andconcentrated under reduced pressure to provide Intermediate 20-c as awhite solid.

Step 3: Intermediate 20-d

To a solution of Intermediate 20-c (2.8 g, 10.7 mmol) in DMF (42.7 ml)was added sodium azide (1.0 g, 16.0 mmol) and the reaction was stirredat 85° C. overnight and then cooled to room temperature. A saturatedaqueous solution of ammonium chloride and diethyl ether were added, theorganic layer was separated, washed with a saturated aqueous solution ofammonium chloride and brine, dried over anhydrous MgSO₄, filtered andconcentrated under reduced pressure to provide Intermediate 20-d aswhite solid.

Step 4: Intermediate 20-e

To a solution of Intermediate 20-d (2.1 g, 9.9 mmol) in methanol (30 ml)and stirred under nitrogen was added 10% Pd/C (211 g, 0.2 mmol). Thereaction mixture was purged with H₂ and stirred for 3 hours under H₂.The reaction was then filtered through celite and the filtrate wasconcentrated in vacuo to provide Intermediate 20-e as a white solid.

Synthesis of Intermediate 21-f

Step 1: Intermediate 21-b

To a solution of cyclohexanecarboxylic acid (6.9 g, 53.8 mmol) in DMF(160 ml) cooled to 0° C. were sequentially added, HBTU (22.1 g, 58.3mmol) and after stirring for 30 minutes, a solution of4-fluoro-3-nitroaniline 21-a (7.0 g, 44.8 mmol) and DiPEA (23.4 ml,135.0 mmol) in DMF (80 ml) was added. The reaction was then stirred for5 days at room temperature. A saturated aqueous solution of ammoniumchloride and ethyl acetate were added, the organic layer was separated,washed with a saturated aqueous solution of ammonium chloride and brine,dried over anhydrous MgSO₄, filtered and concentrated under reducedpressure. Purification by silica gel chromatography providedIntermediate 21-b as a yellow solid.

Step 2: Intermediate 21-c

To a suspension of NaH (60% dispersion in mineral oil, 265 mg, 6.6 mmol)in DMF was added Intermediate 21-b (1.0 g, 3.8 mmol) and after stirringfor 15 minutes at room temperature iodomethane (552 μl, 8.9 mmol) wasadded. After the addition was completed, the reaction was stirred at 60°C. for 2 hours and then cooled to room temperature. Volatiles wereremoved under reduced pressure. An aqueous solution of 1N HCl and ethylacetate were added to the residue, the organic layer was separated,washed with a saturated aqueous solution of NaHCO₃ and brine, dried overanhydrous MgSO₄, filtered and concentrated under reduced pressure toprovide Intermediate 21-c as a beige oil.

Step 3: Intermediate 21-d

A solution of Intermediate 21-c (205 mg, 0.7 mmol), Intermediate 20-e(136 mg, 9.3 mmol) and DIPEA (382 μl, 2.2 mmol) in DMSO was heated at100° C. for 1 h 30 minutes and then cooled to room temperature. Asaturated aqueous solution of ammonium chloride and ethyl acetate wereadded, the organic layer was separated, washed with a saturated aqueoussolution of ammonium chloride and brine, dried over anhydrous MgSO₄,filtered and concentrated under reduced pressure to provide Intermediate21-d as a yellow solid.

Step 4: Intermediate 21-e

To a solution of Intermediate 21-d (330 mg, 0.7 mmol) in methanol andstirred under nitrogen was added 10% Pd/C (16 mg, 0.15 mmol). Thereaction mixture was purged with H₂ and stirred for 1 day under H₂. Thereaction was then filtered through celite and the filtrate wasconcentrated in vacuo to provide Intermediate 21-e as a beige solid.

Step 4: Intermediate 21-f

To a solution of Intermediate 21-e (310 mg, 0.7 mmol) in EtOH (7.4 ml)was added cyanogen bromide (95 mg, 0.9 mmol) and the reaction wasstirred for 5 hours at room temperature. Volatiles were removed underreduced pressure. A saturated aqueous solution of ammonium chloride andethyl acetate were then added to the residue, the organic layer wasseparated, washed with a saturated aqueous solution of NaHCO₃ and brine,dried over anhydrous MgSO₄, filtered and concentrated under reducedpressure to provide Intermediate 21-f as a beige solid.

Synthesis of Intermediate 22-b

Step 1: Intermediate 22-a

To a solution of 5-(difluoromethyl)thiophene-2-carboxylic acid 2-a (200mg, 1.1 mmol) in DMF (3.2 ml) cooled to 0° C. was added HATU (483 mg,1.3 mmol) and after stirring for 30 minutes a solution of Intermediate21-f (330 mg, 0.7 mmol) and DIPEA (522 μl, 3.0 mmol) in DMF (3.2 ml) wasadded dropwise. The reaction was then stirred at room temperatureovernight. A saturated aqueous solution of ammonium chloride and ethylacetate were then added, the organic layer was separated, washed with asaturated aqueous solution of ammonium chloride and brine, dried overanhydrous MgSO₄, filtered and concentrated under reduced pressure.Purification by silica gel chromatography provided Intermediate 22-a asa beige solid.

Step 2: Intermediate 22-b

To a solution of Intermediate 22-a (253 mg, 0.4 mmol) in MeOH (1 ml) wasadded 4N HCl in 1,4-dioxane (13.8 ml, 55.1 mmol) at room temperature andthe solution was stirred at room temperature overnight. Volatiles wereremoved under reduced pressure and the residue was dried under vacuum toprovide Intermediate 22-b.HCl as beige solid.

Synthesis of Compound 63

To a solution of Intermediate 22-b.HCl (211 mg, 0.4 mmol) intetrahydrofuran (4.2 ml) and NMP (1 ml) cooled to −78° C. weresequentially added DIPEA (733 μl, 4.2 mmol) and acryloyl chloride (41μl, 0.5 mmol) and the reaction was stirred at −78° C. for 2 hours. Water(20 mL) and ethyl acetate (20 mL) were added; the organic layer wasseparated, washed with a saturated aqueous solution of NaHCO₃ and brine,dried over anhydrous MgSO₄, filtered and concentrated under reducedpressure. Purification by silica gel chromatography provided Compound 63as a white solid.

Synthesis of Intermediate 24-c

Step 1: Intermediate 24-a

A solution of Intermediate 21-b (200 mg, 0.7 mmol), Intermediate 20-e(140 mg, 07 mmol) and DIPEA (392 μl, 2.2 mmol) in DMSO was heated at100° C. for 3 h 30 minutes and then cooled to room temperature. Asaturated aqueous solution of ammonium chloride and ethyl acetate wereadded, the organic layer was separated, washed with a saturated aqueoussolution of ammonium chloride and brine, dried over anhydrous MgSO₄,filtered and concentrated under reduced pressure to provide Intermediate24-a as a yellow solid.

Step 2: Intermediate 24-b

To a solution of Intermediate 24-a (270 mg, 0.6 mmol) in methanol andstirred under nitrogen was added 10% Pd/C (30 mg, 0.03 mmol). Thereaction mixture was purged with H₂ and stirred for 24 hours under H₂.The reaction was then filtered through celite and the filtrate wasconcentrated under reduced pressure to provide Intermediate 24-b as abeige solid.

Step 3: Intermediate 24-c

To a solution of Intermediate 24-b (230 mg, 0.6 mmol) in EtOH (5.7 ml)was added cyanogen bromide (73 mg, 0.7 mmol) and the reaction wasstirred for 3 hours at room temperature. Volatiles were removed underreduced pressure. A saturated aqueous solution of ammonium chloride andethyl acetate were then added to the residue, the organic layer wasseparated, washed with a saturated aqueous solution of NaHCO₃ and brine,dried over anhydrous MgSO₄, filtered and concentrated under reducedpressure to provide Intermediate 24-c as a beige solid.

Synthesis of Intermediate 25-b

Step 1: Intermediate 25-a

To a solution of 5-(difluoromethyl)thiophene-2-carboxylic acid 2-a (75mg, 0.4 mmol) in DMF (1.2 ml) cooled to 0° C. was added HATU (181 mg,0.4 mmol) and after stirring for 30 minutes a solution of Intermediate24-c (120 mg, 0.3 mmol) and DIPEA (196 μl, 1.1 mmol) in DMF (1.2 ml) wasadded dropwise. The reaction was then stirred at room temperature for 1day. A saturated aqueous solution of ammonium chloride and ethyl acetatewere then added, the organic layer was separated, washed with asaturated aqueous solution of ammonium chloride and brine, dried overanhydrous MgSO₄, filtered and concentrated under reduced pressure.Purification by silica gel chromatography provided Intermediate 25-a asa beige solid.

Step 2: Intermediate 25-b

To a solution of Intermediate 25-a (18 mg, 0.02 mmol) in MeOH (500 μl)was added 4N HCl in dioxane (1.0 ml, 4.0 mmol) at room temperature andthe solution was stirred overnight. Volatiles were removed under reducedpressure and the residue was dried under vacuum to provide Intermediate25-b.HCl as beige solid.

Synthesis of Compound 64

To a solution of Intermediate 25-b.HCl (18 mg, 0.04 mmol) intetrahydrofuran (370 μl) cooled to −78° C. were sequentially added DIPEA(64 μl, 0.4 mmol) and acryloyl chloride (3.6 μl, 0.04 mmol) and thereaction was stirred at −78° C. for 30 minutes. Water (20 mL) and ethylacetate (20 mL) were added; the organic layer was separated, washed witha saturated aqueous solution of NaHCO₃ and brine, dried over anhydrousMgSO₄, filtered and concentrated under reduced pressure. Purification bysilica gel chromatography provided Compound 64 as a white solid.

Synthesis of Intermediate 27-f

Step 1: Intermediate 27-b

To a solution of 4-fluoro-3-nitrobenzoic acid 27-a (10.0 g, 54.0 mmol)in DMF (160 ml) cooled to 0° C. were sequentially added HATU (22.2 g,58.5 mmol), cyclohexanamine (5.2 ml, 45.0 mmol) and DIPEA (23.5 ml,135.0 mmol). The reaction was stirred at room temperature for 1 day. Asaturated aqueous solution of ammonium chloride and ethyl acetate wereadded, the organic layer was separated, washed with a saturated aqueoussolution of ammonium chloride and brine, dried over anhydrous MgSO₄,filtered and concentrated under reduced pressure. Purification by silicagel chromatography provided Intermediate 27-b as a yellow solid.

Step 2: Intermediate 27-c

To a suspension of NaH (60% dispersion in mineral oil, 397 mg, 9.9 mmol)in DMF was added Intermediate 27-b (1.5 g, 5.6 mmol) and after stirringfor 15 minutes at room temperature iodomethane (828 μl, 13.3 mmol) wasadded. After the addition was completed, the reaction was stirred at 60°C. for 1 hour and then cooled to room temperature. Volatiles wereremoved under reduced pressure. An aqueous solution of 1N HCl and ethylacetate were added to the residue, the organic layer was separated,washed with a saturated aqueous solution of NaHCO₃ and brine, dried overanhydrous MgSO₄, filtered and concentrated under reduced pressure toprovide Intermediate 27-c as an orange oil.

Step 3: Intermediate 27-d

A solution of Intermediate 27-c (211 mg, 0.7 mmol), Intermediate 20-e(140 mg, 0.7 mmol) and DIPEA (393 μl, 2.2 mmol) in acetonitrile wasstirred at room temperature for 1 day. A saturated aqueous solution ofammonium chloride and ethyl acetate were added, the organic layer wasseparated, washed with a saturated aqueous solution of ammonium chlorideand brine, dried over anhydrous MgSO₄, filtered and concentrated underreduced pressure to provide Intermediate 27-d as an orange solid.

Step 4: Intermediate 27-e

To a solution of Intermediate 27-d (336 mg, 0.7 mmol) in methanol andstirred under nitrogen was added 10% Pd/C (40 mg, 0.04 mmol). Thereaction mixture was purged with H₂ and stirred for 1 day under H₂. Thereaction was then filtered through celite and the filtrate wasconcentrated in vacuo to provide Intermediate 27-e as a purple oil.

Step 5: Intermediate 27-f

To a solution of Intermediate 27-e (270 mg, 0.6 mmol) in EtOH (6.5 ml)was added cyanogen bromide (82 mg, 0.8 mmol) and the reaction wasstirred for 3 hours at room temperature. Volatiles were removed underreduced pressure. A saturated aqueous solution of ammonium chloride andethyl acetate were then added to the residue, the organic layer wasseparated, washed with a saturated aqueous solution of NaHCO₃ and brine,dried over anhydrous MgSO₄, filtered and concentrated under reducedpressure to provide Intermediate 27-f as a beige solid.

Synthesis of Intermediate 28-b

Step 1: Intermediate 28-a

To a solution of 5-(difluoromethyl)thiophene-2-carboxylic acid 2-a (61mg, 0.34 mmol) in DMF (1.0 ml) cooled to 0° C. was added HATU (146 mg,0.38 mmol) and after stirring for 30 minutes a solution of Intermediate27-f (100 mg, 0.22 mmol) and DIPEA (119 μl, 0.68 mmol) in DMF (1.0 ml)was added dropwise. The reaction was then stirred at room temperaturefor 1 day. A saturated aqueous solution of ammonium chloride and ethylacetate were then added, the organic layer was separated, washed with asaturated aqueous solution of ammonium chloride and brine, dried overanhydrous MgSO₄, filtered and concentrated under reduced pressure.Purification by silica gel chromatography provided Intermediate 28-a asa white solid.

Step 2: Intermediate 28-b

To a solution of Intermediate 28-a (73 mg, 0.12 mmol) in MeOH (500 μl)was added 4N HCl in 1,4-dioxane (3.0 ml, 12.0 mmol) at room temperatureand the solution was stirred overnight. Volatiles were removed underreduced pressure and the residue was dried under vacuum to provideIntermediate 28-b.HCl as white solid.

Synthesis of Compound 65

To a solution of Intermediate 28-b.HCl (60 mg, 0.12 mmol) intetrahydrofuran (1.2 ml) cooled to −78° C. were sequentially added DIPEA(208 μl, 1.2 mmol) and acryloyl chloride (xx μl, 0.14 mmol) and thereaction was stirred at −78° C. for 30 minutes. Water (20 mL) and ethylacetate (20 mL) were added; the organic layer was separated, washed witha saturated aqueous solution of NaHCO₃ and brine, dried over anhydrousMgSO₄, filtered and concentrated under reduced pressure. Purification bysilica gel chromatography provided Compound 65 as a white solid.

Compound 48 was prepared in a similar manner to Compound 65 by replacingIntermediate 20-e with tert-butyl 3-aminophenylcarbamate 1-b for thesynthesis of Intermediate 27-f.

Synthesis of Intermediate 30-c

Step 1: Intermediate 30-a

A solution of Intermediate 27-b (1.0 g, 3.8 mmol), Intermediate 20-e(699 mg, 3.8 mmol) and DIPEA (1.9 ml, 11.3 mmol) in acetonitrile wasstirred at room temperature for 1 day. A saturated aqueous solution ofammonium chloride and ethyl acetate were added, the organic layer wasseparated, washed with a saturated aqueous solution of ammonium chlorideand brine, dried over anhydrous MgSO₄, filtered and concentrated underreduced pressure to provide Intermediate 30-a as a yellow solid.

Step 2: Intermediate 30-b

To a solution of Intermediate 30-a (1.2 g, 2.8 mmol) in methanol (28.0ml) and stirred under nitrogen was added 10% Pd/C (300 mg, 0.28 mmol).The reaction mixture was purged with H₂ and stirred for 1 day under H₂.The reaction was then filtered through celite and the filtrate wasconcentrated under reduced pressure to provide Intermediate 30-b as abeige solid.

Step 3: Intermediate 30-c

To a solution of Intermediate 30-b (410 mg, 1.0 mmol) in EtOH (10.2 ml)was added cyanogen bromide (129 mg, 1.2 mmol) and the reaction wasstirred for 4 hours at room temperature. Volatiles were removed underreduced pressure. A saturated aqueous solution of ammonium chloride andethyl acetate were then added to the residue, the organic layer wasseparated, washed with a saturated aqueous solution of NaHCO₃ and brine,dried over anhydrous MgSO₄, filtered and concentrated under reducedpressure to provide Intermediate 30-c as a beige solid.

Synthesis of Intermediate 31-b

Step 1: Intermediate 31-a

To a solution of 5-(difluoromethyl)thiophene-2-carboxylic acid 2-a (275mg, 1.5 mmol) in DMF (4.4 ml) cooled to 0° C. was added HATU (665 mg,1.8 mmol) and after stirring for 30 minutes a solution of Intermediate30-c (440 mg, 1.0 mmol) and DIPEA (719 μl, 4.1 mmol) in DMF (4.4 ml) wasadded dropwise. The reaction was then stirred at room temperature for 1day. A saturated aqueous solution of ammonium chloride and ethyl acetatewere then added, the organic layer was separated, washed with asaturated aqueous solution of ammonium chloride and brine, dried overanhydrous MgSO₄, filtered and concentrated under reduced pressure.Purification by silica gel chromatography provided Intermediate 31-a asa yellow solid.

Step 2: Intermediate 31-b

To a solution of Intermediate 31-a (17 mg, 0.03 mmol) in MeOH (500 μl)was added 4N HCl in dioxane (947 μl, 3.8 mmol) at room temperature andthe solution was stirred overnight. Volatiles were removed under reducedpressure and the residue was dried under vacuum to provide Intermediate31-b.HCl as white solid.

Synthesis of Compound 70

To a solution of Intermediate 31-b (15 mg, 0.03 mmol) in tetrahydrofuran(300 μl) cooled to −78° C. were sequentially added DIPEA (54 μl, 0.3mmol) and acryloyl chloride (3.0 μl, 0.04 mmol) and the reaction wasstirred at −78° C. for 30 minutes. Water (20 mL) and ethyl acetate (20mL) were added; the organic layer was separated, washed with a saturatedaqueous solution of NaHCO₃ and brine, dried over anhydrous MgSO₄,filtered and concentrated under reduced pressure. Purification by silicagel chromatography provided Compound 70 as a white solid.

Compounds 53 was prepared in a similar manner to Compound 70 byreplacing Intermediate 20-e with tert-butyl 3-aminophenylcarbamate 1-bfor the synthesis of Intermediate 30-c.

Synthesis of Intermediate 33-f

Step 1: Intermediate 33-b

To a solution of 4-iodo-3-nitroaniline 33-a (1.0 g, 3.8 mmol) indichloromethane (10.8 ml) were sequentially added DIPEA (1320 μl, 7.6mmol) and methanesulfonyl chloride (650 μl, 8.4 mmol). After theaddition was completed, the reaction was stirred for 1 hour at roomtemperature. A saturated aqueous solution of ammonium chloride and ethylacetate were added; the organic layer was separated, washed with brine,dried over anhydrous MgSO₄, filtered and concentrated under reducedpressure. Ethyl acetate was added; the organic layer was separated,washed with brine, dried over anhydrous MgSO₄, filtered and concentratedunder reduced pressure to provide Intermediate 33-b as a white solid.

Step 2: Intermediate 33-c

To a solution of Intermediate 33-b (520 mg, 1.5 mmol) in acetonitrile(4.3 ml) were sequentially added K₂CO₃ (630 mg, 4.6 mmol) and methyliodide (285 μl, 4.6 mmol). The reaction was stirred at room temperaturefor 2 days and then filtered. The filtrate was concentrated to halfvolume under reduced pressure, a saturated aqueous solution of ammoniumchloride and dichloromethane were added; the organic layer wasseparated, washed with brine, dried over anhydrous MgSO₄, filtered andconcentrated under reduced pressure to provide Intermediate 33-c as ayellow solid.

Step 3: Intermediate 33-d

A degassed solution of tert-butyl 3-aminophenylcarbamate 1-b (639 mg,3.1 mmol), Intermediate 33-c (500 mg, 1.5 mmol), Cs₂CO₃ (1.4 g, 4.4mmol), X-Phos (70 mg, 0.15 mmol) and Pd₂dba₃ (37 mg, 0.07 mmol) in1,4-dioxane (14.6 ml) was heated at 100° C. for 1 day and then cooled toroom temperature. A saturated aqueous solution of ammonium chloride andethyl acetate were then added, the organic layer was separated, washedwith a saturated aqueous solution of ammonium chloride and brine, driedover anhydrous MgSO₄, filtered and concentrated under reduced pressure.Purification by silica gel chromatography provided Intermediate 33-d asbeige solid.

Step 4: Intermediate 33-e

To a solution of Intermediate 33-d (349 mg, 0.8 mmol) in methanol andstirred under nitrogen was added 10% Pd/C (17 mg, 0.08 mmol). Thereaction mixture was purged with H₂ and stirred for 1 day under H₂. Thereaction was then filtered through celite and the filtrate wasconcentrated in vacuo to provide Intermediate 33-e as a beige solid.

Step 5: Intermediate 33-f

To a solution of Intermediate 33-e (322 mg, 0.8 mmol) in EtOH (7.9 ml)was added cyanogen bromide (105 mg, 1.0 mmol) and the reaction wasstirred at room temperature overnight. Volatiles were removed underreduced pressure. A saturated aqueous solution of ammonium chloride andethyl acetate were then added to the residue, the organic layer wasseparated, washed with a saturated aqueous solution of NaHCO₃ and brine,dried over anhydrous MgSO₄, filtered and concentrated under reducedpressure. Purification by silica gel chromatography providedIntermediate 33-f as purple foam.

Synthesis of Intermediate 34-b

Step 1: Intermediate 34-a

To a solution of 5-(difluoromethyl)thiophene-2-carboxylic acid 2-a (52mg, 0.3 mmol) in DMF (1.3 ml) was added HATU (132 mg, 0.3 mmol) andafter stirring for 30 minutes a solution of Intermediate 33-f (115 mg,0.3 mmol) and DIPEA (140 μl, 0.8 mmol) in DMF (2.0 ml) was addeddropwise. The reaction was then stirred at room temperature for 1 day. Asaturated aqueous solution of ammonium chloride and ethyl acetate werethen added, the organic layer was separated, washed with a saturatedaqueous solution of ammonium chloride and brine, dried over anhydrousMgSO₄, filtered and concentrated under reduced pressure. Purification bysilica gel chromatography provided Intermediate 34-a as a purple solid.

Step 2: Intermediate 34-b

To a solution of Intermediate 34-a (100 mg, 0.17 mmol) in MeOH (2 mL)was added 4N solution of HCl in dioxane (3 ml) and the reaction wasstirred at room temperature for 30 minutes. Volatiles were removed underreduced pressure. Diethyl ether was added to the residue; a precipitateformed and was collected by filtration to provide Intermediate 34-b.HClas a purple solid.

Synthesis of Compound 80

To a solution of Intermediate 34-b (90 mg, 0.17 mmol) in tetrahydrofuran(2.0 ml) cooled to 0° C. were sequentially added DIPEA (35 μl, 0.2 mmol)and acryloyl chloride (14 μl, 0.19 mmol) and the reaction was stirred at0° C. for 30 minutes. Water (20 mL) and ethyl acetate (20 mL) wereadded; the organic layer was separated, washed with a saturated aqueoussolution of NaHCO₃ and brine, dried over anhydrous MgSO₄, filtered andconcentrated under reduced pressure. Purification by silica gelchromatography provided Compound 80 as a white solid.

Synthesis of Compound 72

Step 1: Intermediate 36-a

To a solution of Intermediate 8-b (100 mg, 0.2 mmol) and but-2-ynoicacid (20 mg, 0.2 mmol) in DMF (2.2 ml) were sequentially added DIPEA(194 μl, 1.1 mmol) and HATU (110 mg, 0.3 mmol) and the reaction was thenstirred at room temperature for 1 day. A saturated aqueous solution ofammonium chloride and ethyl acetate were then added, the organic layerwas separated, washed with a saturated aqueous solution of ammoniumchloride and brine, dried over anhydrous MgSO₄, filtered andconcentrated under reduced pressure. Purification by silica gelchromatography provided Intermediate 36-a as an off-white solid.

Step 2: Intermediate 36-b

To a solution of Intermediate 36-a (50 mg, 0.1 mmol) in THF (1.0 ml) andDMSO (74 μl) cooled to 0° C. were sequentially added DIPEA (73 μl, 0.4mmol) and a solution of SO₃ pyridine complex (50 mg, 0.3 mmol) in DMSO(1 mL). The mixture was then stirred at 0° C. for 1 day. Volatiles wereremoved under reduced pressure, water was added, a precipitate formedand was collected by filtration, washed with water and dried undervacuum to provide Intermediate 36-b as beige solid.

Step 3: Compound 72

To a solution of Intermediate 36-b (25 mg, 0.05 mmol) and(S)-3,3-dimethylbutan-2-amine (7.1 μl, 0.05 mmol) in THF (1.0 ml) andacetonitrile (1 ml), were sequentially added 1 drop of acetic acid andsodium triacetoxyborohydride (17 mg, 0.07 mmol) and the reaction wasstirred overnight at room temperature. Volatiles were removed underreduced pressure. Purification by silica gel chromatography providedCompound 72 as white solid.

Compounds 83 and 84 were prepared in a similar manner to Compound 72 byreplacing

with

respectively.

Synthesis of Compound 78

Step 1: Intermediate 37-a

To a solution of (E)-4-bromobut-2-enoic acid (51 mg, 0.3 mmol) indichloromethane cooled to −78° C. were sequentially added oxalylchloride (49 μl, 0.6 mmol) and DMF (217 μl, 2.8 mmol) and the reactionwas stirred at −78° C. for 1 hour. Volatiles were removed under reducedpressure and the residue was dissolved in dichloromethane.

To a solution of Intermediate 8-b (116 mg, 0.3 mmol) in THF (2 ml)cooled to −78° C. was added DIPEA (245 μl, 1.4 mmol) and a solution of(E)-4-bromobut-2-enoyl chloride prepared above and after completion, a1M solution of dimethylamine in THF (2.8 ml, 2.8 mmol) was added and thereaction was then stirred at room temperature overnight. Volatiles wereremoved under reduced pressure. Purification by silica gelchromatography provided Intermediate 37-a as a beige solid.

Step 2: Intermediate 37-b

To a solution of Intermediate 37-a (110 mg, 0.2 mmol) in THF (1.7 ml)and DMSO (122 μl) cooled to 0° C. were sequentially added DIPEA (150 μl,0.8 mmol) and a solution of SO₃ pyridine complex (82 mg, 0.5 mmol) inDMSO (1 mL). The mixture was then stirred at 0° C. overnight. Volatileswere removed under reduced pressure, water was added, a precipitateformed and was collected by filtration, washed with water and driedunder vacuum to provide Intermediate 37-b as a beige solid.

Step 3: Compound 78

To a solution of Intermediate 37-b (90 mg, 0.2 mmol) and(S)-3,3-dimethylbutan-2-amine 1-d (27 μl, 0.2 mmol) in1,2-dichloroethane (2.0 ml), were sequentially added 1 drop of aceticacid and sodium triacetoxyborohydride (55 mg, 0.2 mmol) and the reactionwas stirred overnight at room temperature. Volatiles were removed underreduced pressure. Purification by silica gel chromatography providedCompound 78 as white solid.

Synthesis of Intermediate 38-e

Step 1: Intermediate 38-b

To a solution of 4-iodo-3-nitrophenol 38-a (3.0 g, 11.3 mmol) in acetone(113 ml) was added potassium carbonate (1.5 g, 11.3 mmol) and afterstirring for 5 minutes, benzyl bromide (1.3 ml, 11.3 mmol) was added.The reaction was stirred at reflux for 4 hours, then cooled to roomtemperature and filtered. Volatiles were removed under reduced pressureto provide Intermediate 38-b as a yellow solid.

Step 2: Intermediate 38-c

A degassed solution of tert-butyl 3-aminophenylcarbamate 1-b (1.2 g, 5.9mmol), Intermediate 38-b (1.0 g, 2.8 mmol), Cs₂CO₃ (2.7 g, 8.4 mmol),X-Phos (100 mg, 0.3 mmol) and Pd₂dba₃ (129 mg, 0.14 mmol) in dioxane(28.1 ml) was heated at 100° C. for 1 day and then cooled to roomtemperature. A saturated aqueous solution of ammonium chloride and ethylacetate were then added, the organic layer was separated, washed with asaturated aqueous solution of ammonium chloride and brine, dried overanhydrous MgSO₄, filtered and concentrated under reduced pressure.Purification by silica gel chromatography provided Intermediate 38-c asa red solid.

Step 3: Intermediate 38-d

To a solution of Intermediate 38-c (1.2 g, 2.8 mmol) in methanol (28.0ml) and stirred under nitrogen was added 10% Pd/C (298 mg, 0.28 mmol).The reaction mixture was purged with H₂ and stirred for 1 day under H₂.The reaction was then filtered through celite and the filtrate wasconcentrated in vacuo. Purification by silica gel chromatographyprovided Intermediate 38-d as purple solid.

Step 4: Intermediate 38-e

To a solution of Intermediate 38-d (470 mg, 1.1 mmol) in EtOH (11.6 ml)was added cyanogen bromide (184 mg, 1.7 mmol) and the reaction wasstirred for 6 hours at room temperature. Volatiles were removed underreduced pressure. A saturated aqueous solution of ammonium chloride andethyl acetate were then added to the residue, the organic layer wasseparated, washed with a saturated aqueous solution of NaHCO₃ and brine,dried over anhydrous MgSO₄, filtered and concentrated under reducedpressure to provide Intermediate 38-e as a purple solid.

Synthesis of Intermediate 39-b

Step 1: Intermediate 39-a

To a solution of 5-(difluoromethyl)thiophene-2-carboxylic acid 2-a (214mg, 1.2 mmol) in DMF (10.0 ml) cooled to 0° C. was added HATU (494 mg,1.3 mmol) and after stirring for 30 minutes a solution of Intermediate38-e (430 mg, 1.0 mmol) and DIPEA (523 μl, 3.0 mmol) in DMF (2.0 ml) wasadded dropwise. The reaction was then stirred at room temperature for 1day. A saturated aqueous solution of ammonium chloride and ethyl acetatewere then added, the organic layer was separated, washed with asaturated aqueous solution of ammonium chloride and brine, dried overanhydrous MgSO₄, filtered and concentrated under reduced pressure.Purification by silica gel chromatography provided Intermediate 39-a asa purple solid.

Step 2: Intermediate 39-b

To a solution of Intermediate 39-a (100 mg, 0.1 mmol) in dichloromethane(1.0 ml) was added TFA (1.0 ml, 13.1 mmol) at 0° C. and the solution wasstirred at room temperature for 30 minutes. Volatiles were removed underreduced pressure to provide Intermediate 39-b.TFA as a beige oil.

Synthesis of Compound 79

To a solution of Intermediate 39-b TFA (25 mg, 0.05 mmol) intetrahydrofuran (510 μl) cooled to 0° C. were sequentially added DIPEA(89 μl, 0.5 mmol) and acryloyl chloride (8.2 μl, 0.1 mmol) and thereaction was stirred at 0° C. for 30 minutes. Water (20 mL) and ethylacetate (20 mL) were added; the organic layer was separated, washed witha saturated aqueous solution of NaHCO₃ and brine, dried over anhydrousMgSO₄, filtered and concentrated under reduced pressure. Purification bysilica gel chromatography provided Compound 79 as an off-white solid.

Synthesis of Intermediate 41-e

Step 1: Intermediate 41-b

To a solution of Intermediate 41-a (1.4 g, 5.0 mmol) in dichloromethane(25 ml) were sequentially added a saturated aqueous solution of NaHCO₃(25.0 ml) and benzyl chloroformate (1.4 ml, 10.1 mmol) and the reactionwas then stirred at room temperature until completion. A saturatedaqueous ammonium chloride solution and ethyl acetate were added; theorganic layer was separated, washed with a saturated aqueous solution ofammonium chloride and brine, dried over anhydrous MgSO₄, filtered andconcentrated under reduced pressure to provide Intermediate 41-b as ayellow solid.

Step 2: Intermediate 41-c

A degassed solution of tert-butyl 3-aminophenylcarbamate 1-b (2.1 g,10.2 mmol), Intermediate 41-b (2.0 g, 4.8 mmol), Cs₂CO₃ (4.7 g, 14.6mmol), X-Phos (231 mg, 0.5 mmol) and Pd₂dba₃ (222 mg, 0.24 mmol) indioxane (48.5 ml) was heated at 100° C. for 1 day and then cooled toroom temperature. A saturated aqueous solution of ammonium chloride andethyl acetate were then added, the organic layer was separated, washedwith a saturated aqueous solution of ammonium chloride and brine, driedover anhydrous MgSO₄, filtered and concentrated under reduced pressure.Purification by silica gel chromatography provided Intermediate 41-c asyellow solid.

Step 3: Intermediate 41-d

To a solution of Intermediate 41-c (820 mg, 1.7 mmol) in MeOH (11.1 ml)was added a saturated aqueous solution of ammonium chloride (3.0 ml) andzinc dust (544 mg, 8.3 mmol) portion wise. The reaction was then stirredat 50° C. for 2 hours, then cooled to room temperature and filtered overcelite. The filtrate was concentrated under reduced pressure. Diethylether and a saturated aqueous solution of ammonium chloride were addedto the residue, the organic layer was separated, washed with brine,dried over MgSO₄, filtered and concentrated under reduced pressure.Purification by silica gel chromatography provided Intermediate 41-d asa purple solid.

Step 3: Intermediate 41-e

To a solution of Intermediate 41-d (468 mg, 1.0 mmol) in EtOH (20.2 ml)was added cyanogen bromide (129 mg, 1.2 mmol) and the reaction wasstirred overnight at room temperature. Volatiles were removed underreduced pressure. A saturated aqueous solution of ammonium chloride andethyl acetate were then added to the residue, the organic layer wasseparated, washed with a saturated aqueous solution of NaHCO₃ and brine,dried over anhydrous MgSO₄, filtered and concentrated under reducedpressure to provide Intermediate 41-e as a purple foam.

Synthesis of Intermediate 42-b

Step 1: Intermediate 42-a

To a solution of 5-(difluoromethyl)thiophene-2-carboxylic acid 2-a (67mg, 0.4 mmol) in DMF (1.7 ml) cooled to 0° C. was added HATU (168 mg,0.4 mmol) and after stirring for 30 minutes a solution of Intermediate41-e (166 mg, 0.3 mmol) and DIPEA (178 μl, 0.4 mmol) in DMF (2.0 ml) wasadded dropwise. The reaction was then stirred at room temperature for 4hours. A saturated aqueous solution of ammonium chloride and ethylacetate were then added, the organic layer was separated, washed with asaturated aqueous solution of ammonium chloride and brine, dried overanhydrous MgSO₄, filtered and concentrated under reduced pressure.Purification by silica gel chromatography provided Intermediate 42-a asa purple solid.

Step 2: Intermediate 42-b

To a solution of Intermediate 42-a (125 mg, 0.2 mmol) in methanol (5.0ml) and stirred under nitrogen was added 10% Pd/C (41 mg, 0.02 mmol).The reaction mixture was purged with H₂ and stirred for 24 hours underH₂. The reaction was then filtered through celite and the filtrate wasconcentrated under reduced pressure to provide Intermediate 42-b asbeige solid.

Step 3: Intermediate 42-c

To a solution of (S)-2-morpholinopropanoic acid (15 mg, 0.09 mmol) inDMF (400 μl) cooled to 0° C. was added HATU (41 mg, 0.1 mmol) and afterstirring for 30 minutes a solution of Intermediate 42-b (52 mg, 0.08mmol) and DIPEA (43 μl, 0.2 mmol) in DMF (2.0 ml) was added dropwise.The reaction was then stirred at room temperature for 1 week. Asaturated aqueous solution of ammonium chloride and ethyl acetate werethen added, the organic layer was separated, washed with a saturatedaqueous solution of ammonium chloride and brine, dried over anhydrousMgSO₄, filtered and concentrated under reduced pressure. Purification bysilica gel chromatography provided Intermediate 42-c as a purple solid.

Step 4: Intermediate 42-d

To a solution of Intermediate 42-c (50 mg, 0.07 mmol) in methanol (2.0ml) was added a 4.0 N solution of HCl in 1,4-dioxane (5 ml, 20 mmol) at0° C. and the solution was stirred at room temperature for 30 minutes.Volatiles were removed under reduced pressure to provide Intermediate42-d HCl as a purple solid.

Synthesis of Compound 77

To a solution of Intermediate 42-d HCl (50 mg, 0.08 mmol) intetrahydrofuran (2.0 ml) cooled to 0° C. were sequentially added DIPEA(69 μl, 0.4 mmol) and acryloyl chloride (6.4 μl, 0.08 mmol) and thereaction was stirred at 0° C. for 30 minutes. Water and ethyl acetatewere added; the organic layer was separated, washed with a saturatedaqueous solution of NaHCO₃ and brine, dried over anhydrous MgSO₄,filtered and concentrated under reduced pressure. Purification by silicagel chromatography provided Compound 77 as a white solid.

Synthesis of Compound 36

To a solution of compound 2 (80 mg, 0.1 mmol) in dichloromethane (1.5ml) cooled to 0° C. were sequentially added TEA (201 μl, 1.5 mmol) andacetyl chloride (12 μl, 0.17 mmol) and the reaction was then stirred atroom temperature for 3 hours. Water (20 mL) and ethyl acetate (20 mL)were added; the organic layer was separated, washed with a saturatedaqueous solution of NaHCO₃ and brine, dried over anhydrous MgSO₄,filtered and concentrated under reduced pressure. Purification by silicagel chromatography provided Compound 36 as a beige solid.

TABLE 1 Example Compounds of Formula I Compound Structure MS (m/z)  1

[M + H]⁺ = 530.3  2

[M + H]⁺ = 552.3  3

[M + H]⁺ = 558.3  4

[M + H]⁺ = 552.4  5

[M + H]⁺ = 566.4  6

[M + H]⁺ = 544.3  7

[M + H]⁺ = 514.3  8

[M + H]⁺ = 526.4  9

[M + H]⁺ = 521.2 10

[M + H]⁺ = 530.6 11

[M + H]⁺ = 521.4 12

[M + H]⁺ = 503.3 13

[M + H]⁺ = 502.3 14

[M + H]⁺ = 550.3 15

[M + H]⁺ = 531.2 16

[M + H]⁺ = 497.2 17

[M + H]⁺ = 503.3 18

[M + H]⁺ = 544.2 19

[M + H]⁺ = 497.4 20

[M + H]⁺ = 514.3 21

[M + H]⁺ = 524.3 22

[M + H]⁺ = 568.3 23

[M + H]⁺ = 538.3 24

[M + H]⁺ = 526.4 25

[M + H]⁺ = 569.3 26

[M + H]⁺ = 512.3 27

[M + H]⁺ = 497.3 28

[M + H]⁺ = 500.4 29

[M + H]⁺ = 554.3 30

[M + H]⁺ = 552.3 31

[M + H]⁺ = 566.3 32

[M + H]⁺ = 522.3 33

[M + H]⁺ = 570.3 34

[M + H]⁺ = 570.3 35

[M + H]⁺ = 566.3 36

[M + H]⁺ = 594.3 37

[M + H]⁺ = 602.3 38

[M + H]⁺ = 487.3 39

[M + H]⁺ = 526.7 40

[M + H]⁺ = 496.2 41

[M + H]⁺ = 498.3 42

[M + H]⁺ = 487.1 43

[M + H]⁺ = 503.3 44

[M + H]⁺ = 552.3 45

[M + H]⁺ = 552.2 46

[M + H]⁺ = 570.2 47

[M + H]⁺ = 568.2 48

[M + H]⁺ = 578.3 49

[M + H]⁺ = 500.2 50

[M + H]⁺ = 538.2 51

[M + H]⁺ = 624.1 52

[M + H]⁺ = 624.1 53

[M + H]⁺ = 564.2 54

[M + H]⁺ = 527.4 55

[M + H]⁺ = 503.4 56

[M + H]⁺ = 578.3 57

[M + H]⁺ = 594.4 58

[M + H]⁺ = 572.3 59

[M + H]⁺ = 581.2 60

[M + H]⁺ = 624.1 61

[M + H]⁺ = 566.2 62

[M + H]⁺ = 544.2 63

[M + H]⁺ = 556.3 64

[M + H]⁺ = 542.2 65

[M + H]⁺ = 556.2 66

[M + H]⁺ = 669.2 67

[M + H]⁺ = 509.3 68

[M + H]⁺ = 558.3 69

[M + H]⁺ = 469.2 70

[M + H]⁺ = 542.2 71

[M + H]⁺ = 575.4 72

[M + H]⁺ = 564.3 73

[M + H]⁺ = 489.2 74

[M + H]⁺ = 501.2 75

[M + H]⁺ = 517.2 76

[M + H]⁺ = 473.3 77

[M + H]⁺ = 609.2 78

[M + H]⁺ = 609.2 79

[M + H]⁺ = 545.1 80

[M + H]⁺ = 546.1 81

[M + H]⁺ = 558.3 82

[M + H]⁺ = 545.3 83

[M + H]⁺ = 566.2 84

[M + H]⁺ = 570.2 85

[M + H]⁺ = 467.1 86

[M + H]⁺ = 413.4 87

[M + H]⁺ = 402.4 88

[M + H]⁺ = 418.4

The compounds in the table above form part of the invention in additionto pharmaceutically acceptable salts thereof.

Some of the above compounds have one or more chiral centres, for exampleone or two chiral centres. All enantiomers and diastereomers of theabove compounds are contemplated by the invention. In one embodiment thecompounds of the invention have the (R)-configuration at thestereocentre. In an alternative embodiment the compounds of theinvention have the (S)-configuration at the stereocentre. Wherecompounds have two stereocentres the stereocentres may have (R),(R)configuration, (S),(R) configuration, (R),(S) configuration or (S),(S)configuration. The invention also contemplates racemic mixtures of thesecompounds.

Assays for determining kinase activity are described in more detail inthe accompanying examples.

Example 2: CD3/CD28 Mediated PBMC Proliferation Assay

Inhibition of cellular ITK was assessed by measuring proliferation ofPBMCs following stimulation with anti-CD3 and anti-CD28 antibodies.Individual wells of 96 well tissue culture plates were coated with 50 μLof 5 μg/mL anti-CD3 (OKT3, eBiosciences) for 2 hours at 37° C. HumanPBMCs (Stemcell Technologies catalog #70025.3) were plated in 96-wellplates at a final concentration of 9.2×10e5 cells/mL in complete media(RPMI, 10% heat inactivated FBS, 55 uM β-mercaptoethanol) andpre-treated with compound curves for 30 minutes at 37° C., 5% CO₂.Pre-treated cells plus compounds were transferred to washed anti-CD3coated plates. Soluble anti-CD28 (CD28.2 eBiosciences) was added to eachwell at a final concentration of 2 μg/mL. The cells were placed in ahumidified 37° C. incubator with 5% CO₂ for 72 hours and metabolicviability was measured by quantification of ATP levels with CellTiter-Glo (Promega catalog #G9242). Controls included unstimulated cellsand vehicle alone. EC50 values (50% proliferation in the presence ofcompound as compared to vehicle treated controls) were calculated fromdose response compound curves using GraphPad Prism Software.

TABLE 2 Results Compound EC₅₀(nM) 1 b 2 b 3 c 4 c 5 b 6 b 7 b 8 c 9 b 10b 11 b 12 c 13 b 14 b 15 b 16 b 17 b 18 b 19 b 20 c 21 a 22 a 23 a 24 c25 a 26 c 27 c 28 b 29 a 30 a 31 a 32 a 33 a 34 c 35 a 36 b 37 c 38 b 39a 40 a 41 b 42 b 43 a 44 a 45 a 46 b 47 a 48 b 49 c 50 a 51 a 52 a 53 b54 c 55 c 56 b 57 b 58 c 59 a 60 a 61 a 62 c 63 c 64 c 65 c 66 b 67 c 68a 69 b 70 c 71 b 72 c 73 b 74 c 75 c 76 b 77 b 78 c 79 c 80 b 81 b 83 c84 b a—EC₅₀ < 10 nM; b—10 nM < EC₅₀ < 100 nM, c—EC₅₀ > 100 nM

Example 3: Jurkat IL-2 Release Assay

Inhibition of cellular ITK was assessed by measuring release of IL-2following stimulation with anti-CD3 and anti-CD28 antibodies. Individualwells of 96 well tissue culture plates were coated with 50 μL of 10μg/mL anti-CD3 (OKT3, eBiosciences) for 2 hours at 37° C. Jurkat humanacute T cell leukemia cells (ATCC) were plated in 96-well plates at afinal concentration of 9.2×10e5 cells/mL in complete media (RPMI, 10%FBS, 1.5 g/L sodium bicarbonate, 10 mM Hepes, 1 mM sodium pyruvate, 4.5g/L glucose) and pre-treated with compound curves for 30 minutes at 37°C., 5% CO₂. Pre-treated cells plus compounds were transferred to washedanti-CD3 coated plates. Soluble anti-CD28 (CD28.2 eBiosciences) wasadded to each well at a final concentration of 1 μg/mL. The cells wereplaced in a humidified 37° C. incubator with 5% CO₂ for 48 hours andIL-2 release was measured using a commercial ELISA (BD Biosciencecatalog #555190). Controls included unstimulated cells and vehiclealone. EC50 values (50% IL-2 release in the presence of compound ascompared to vehicle treated controls) were calculated from dose responsecompound curves using GraphPad Prism Software.

TABLE 4 Results Compound EC₅₀ (nM) 1 b 2 a 3 b 4 b 5 a 6 a 7 b 8 b 9 b10 b 11 c 12 c 13 b 14 a 15 b 16 b 17 b 18 a 19 a 20 b 21 b 22 a 23 a 24c 25 a 26 b 27 c 28 a 29 a 30 b 31 a 32 a 33 a 34 c 35 b 36 b 37 c 38 a39 b 40 b 41 a 42 a 43 a 50 a 54 c 57 b 59 a 62 b 67 b 72 b 73 a 76 a 77a 78 b 80 b 81 a 82 b 84 b a—EC₅₀ < 10 nM; b—10 nM < EC₅₀ < 100 nM,c—EC₅₀ > 100 nM

Example 4: ITK Kinase Inhibition Assay

The in vitro kinase assays were performed at Nanosyn utilizingmicro-fluidic detection technology. The test compounds were seriallypre-diluted in DMSO and added, by the acoustic dispensing (Labcyte®550), directly to 384 well assay plates into 10 uL of a buffer withenzyme comprising: 100 mM HEPES, pH7.5, 5 mM MgCl₂, 0.1% bovine serumalbumin, 1 mM DTT, 0.01% Triton X-100 and the enzyme. Final DMSOconcentration was maintained at 1% in all samples, including thecontrols. The reactions were initiated by addition of ATP (to thespecified concentration) and the fluorescently labeled peptide substrateto a final concentration of 1 uM, and incubated for 3 hours at 25° C.Following incubation, the reactions were quenched by addition of 40 μLof termination buffer (100 mM HEPES, pH7.5, 0.01% Triton X-100, 50 mMEDTA). Terminated plates were analyzed using Caliper LabChip® 3000microfluidic electrophoresis instrument (Caliper Life Sciences/PerkinElmer). The enzymatic modification of the peptide substrate(phosphorylation) results in a change of net charge enablingelectrophoretic separation of product from substrate. As substrate andproduct are separated by electrophoresis, two peaks of fluorescence areobserved. Change in the relative fluorescence intensity of the substrateand product peaks was the parameter measured, reflecting enzymeactivity. In the presence of inhibitor, the ratio between product andsubstrate is altered: signal of the product decreases, while the signalof the substrate increases. Activity in each test sample was determinedas the product to sum ratio (PSR):P/(S+P), where P is the peak height ofthe product and S is the peak height of the FAM-cAMP substrate. For eachcompound, enzyme activity was measured at 12 concentrations spaced by 3×dilution intervals. Negative control samples (0%-inhibition in theabsence of inhibitor, DMSO only) and positive control samples(100%-inhibition, in the absence of enzyme or in the presence of controlinhibitor) were assembled in replicates of four and were used tocalculate %-inhibition values in the presence of compounds. Percentinhibition (P_(inh)) was determined using the following equation:P_(inh)═(PSR_(0%)−PSR_(inh))/(PSR_(0%)−PSR_(100%))*100, where PSR_(inh)is the product sum ratio in the presence of inhibitor, PSR_(0%) is theproduct sum ratio in the absence of inhibitor and PSR_(100%) is theproduct sum ratio in 100%-inhibition control samples. To determine IC₅₀values, the inhibition curves (P_(inh) versus inhibitor concentration)were fitted by 4 parameter sigmoid dose-response model using XLfitsoftware (IDBS).

TABLE 5 Results of ITK kinase inhibition Compound EC₅₀ (nM) 1 a 2 a 3 b9 a 11 a 12 c 16 a 17 b 18 a 19 a 25 a 27 c 28 a 31 a 38 a 42 b 43 a 50a 62 a 68 a 77 a 81 a a—EC₅₀ < 10 nM; b—10 nM < EC₅₀ < 100 nM, c—EC₅₀ >100 nM

Example 5: RLK/TXK Kinase Inhibition Assay

The in vitro kinase assays were performed at Nanosyn utilizingmicro-fluidic detection technology. The test compounds were seriallypre-diluted in DMSO and added, by the acoustic dispensing (Labcyte®550), directly to 384well assay plates into 10 uL of a buffer withenzyme comprising: 100 mM HEPES, pH7.5, 5 mM MgCl₂, 0.1% bovine serumalbumin, 1 mM DTT, 0.01% Triton X-100 and the enzyme. Final DMSOconcentration was maintained at 1% in all samples, including thecontrols. The reactions were initiated by addition of ATP (to thespecified concentration) and the fluorescently labeled peptide substrateto a final concentration of 1 uM, and incubated for 3 hours at 25° C.Following incubation, the reactions were quenched by addition of 40 μLof termination buffer (100 mM HEPES, pH7.5, 0.01% Triton X-100, 50 mMEDTA). Terminated plates were analyzed using Caliper LabChip® 3000microfluidic electrophoresis instrument (Caliper Life Sciences/PerkinElmer). The enzymatic modification of the peptide substrate(phosphorylation) results in a change of net charge enablingelectrophoretic separation of product from substrate. As substrate andproduct are separated by electrophoresis, two peaks of fluorescence areobserved. Change in the relative fluorescence intensity of the substrateand product peaks was the parameter measured, reflecting enzymeactivity. In the presence of inhibitor, the ratio between product andsubstrate is altered: signal of the product decreases, while the signalof the substrate increases. Activity in each test sample was determinedas the product to sum ratio (PSR): P/(S+P), where P is the peak heightof the product and S is the peak height of the FAM-cAMP substrate. Foreach compound, enzyme activity was measured at 12 concentrations spacedby 3× dilution intervals. Negative control samples (0%-inhibition in theabsence of inhibitor, DMSO only) and positive control samples(100%-inhibition, in the absence of enzyme or in the presence of controlinhibitor) were assembled in replicates of four and were used tocalculate %-inhibition values in the presence of compounds. Percentinhibition (P_(inh)) was determined using the following equation:P_(inh)=(PSR_(0%)−PSR_(inh))/(PSR_(0%)−PSR_(100%))*100, where PSR_(inh)is the product sum ratio in the presence of inhibitor, PSR_(0%) is theproduct sum ratio in the absence of inhibitor and PSR_(100%) is theproduct sum ratio in 100%-inhibition control samples. To determine IC₅₀values, the inhibition curves (P_(inh) versus inhibitor concentration)were fitted by 4 parameter sigmoid dose-response model using XLfitsoftware (IDBS).

TABLE 6 Results of RLK/TXK kinase inhibition Compound EC₅₀ (nM) 1 b 2 a3 b 9 a 11 a 12 b 16 a 17 a 18 a 19 b 25 a 27 c 28 a 31 a 38 a 42 b 43 a50 a 62 b 68 a 77 a 81 b a—EC₅₀ < 10 nM; b—10 nM < EC₅₀ < 100 nM,c—EC₅₀ > 100 nM

Example 6: Tec Kinase Inhibition Assay

The in vitro kinase assays were performed at Nanosyn utilizingmicro-fluidic detection technology. The test compounds were seriallypre-diluted in DMSO and added, by the acoustic dispensing (Labcyte®550), directly to 384well assay plates into 10 uL of a buffer withenzyme comprising: 100 mM HEPES, pH7.5, 5 mM MgCl₂, 0.1% bovine serumalbumin, 1 mM DTT, 0.01% Triton X-100 and the enzyme. Final DMSOconcentration was maintained at 1% in all samples, including thecontrols. The reactions were initiated by addition of ATP (to thespecified concentration) and the fluorescently labeled peptide substrateto a final concentration of 1 uM, and incubated for 3 hours at 25° C.Following incubation, the reactions were quenched by addition of 40 μLof termination buffer (100 mM HEPES, pH7.5, 0.01% Triton X-100, 50 mMEDTA). Terminated plates were analyzed using Caliper LabChip® 3000microfluidic electrophoresis instrument (Caliper Life Sciences/PerkinElmer). The enzymatic modification of the peptide substrate(phosphorylation) results in a change of net charge enablingelectrophoretic separation of product from substrate. As substrate andproduct are separated by electrophoresis, two peaks of fluorescence areobserved. Change in the relative fluorescence intensity of the substrateand product peaks was the parameter measured, reflecting enzymeactivity. In the presence of inhibitor, the ratio between product andsubstrate is altered: signal of the product decreases, while the signalof the substrate increases. Activity in each test sample was determinedas the product to sum ratio (PSR): P/(S+P), where P is the peak heightof the product and S is the peak height of the FAM-cAMP substrate. Foreach compound, enzyme activity was measured at 12 concentrations spacedby 3× dilution intervals. Negative control samples (0%-inhibition in theabsence of inhibitor, DMSO only) and positive control samples(100%-inhibition, in the absence of enzyme or in the presence of controlinhibitor) were assembled in replicates of four and were used tocalculate %-inhibition values in the presence of compounds. Percentinhibition (P_(inh)) was determined using the following equation:P_(inh)=(PSR_(0%)−PSR_(inh))/(PSR_(0%)−PSR_(100%))*100, where PSR_(inh)is the product sum ratio in the presence of inhibitor, PSR_(0%) is theproduct sum ratio in the absence of inhibitor and PSR_(100%) is theproduct sum ratio in 100%-inhibition control samples. To determine IC₅₀values, the inhibition curves (P_(inh) versus inhibitor concentration)were fitted by 4 parameter sigmoid dose-response model using XLfitsoftware (IDBS).

TABLE 7 Results of Tec kinase inhibition Compound EC₅₀ (nM) 2 b 9 b 25 a28 b 38 b a—EC₅₀ < 10 nM; b—10 nM < EC₅₀ < 100 nM, c—EC₅₀ > 100 nM

1-50. (canceled)
 51. A method for treating a subject suffering from aprotein kinase mediated disease, disorder, or condition associated withthe activity of at least one kinase member of the Tec kinase family,comprising administering to the subject in need thereof atherapeutically effective amount of a compound having the structure ofFormula I:

or a pharmaceutically acceptable salt, stereoisomer, tautomer, isotope,prodrug, or complex thereof, wherein R is substituted or unsubstitutedthiophenyl; L is

wherein ring B₁ is substituted or unsubstituted cycloalkyl; R¹ ishydrogen, lower alkyl, or lower cycloalkyl; and n is 0 or 1; E is:

wherein: Ra, Rb, and Rc are independently hydrogen, halogen, —CN,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, or substituted orunsubstituted heterocyclyl; or Ra and Rb, taken together with the carbonatoms to which they are attached, form a 3- to 8-membered substituted orunsubstituted cycloalkyl ring or form a 3- to 8-membered substituted orunsubstituted heterocyclic ring and Rc is selected as above; or Rb andRc, taken together with the carbon atom to which they are attached, forma 3- to 8-membered substituted or unsubstituted cycloalkyl ring or forma 3- to 8-substituted or unsubstituted membered heterocyclic ring and Rais selected as above; or Ra and Rb, taken together with the carbon atomsto which they are attached, form a triple bond and Rc is selected asabove; wherein -L-E is:

X is a bond, alkylene, -(alkylene)-NR²—, -(alkylene)-NR³—,-(alkylene)-O—, —O—, —S—, —S(O)_(m)—, —NR²—, —C(O)—, —C(O)O—, —C(O)NR²—,—C(O)ONR²—, or —S(O)_(m)NR²—, wherein: R² is hydrogen, lower alkyl orlower cycloalkyl; R³ is —C(O)R⁴, —C(O)OR⁴ or —S(O)_(m)R⁴; R⁴ is loweralkyl or lower cycloalkyl; m is 1 or 2; and Y is hydrogen, halogen,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocyclyl, substituted or unsubstitutedaryl, substituted or unsubstituted heteroaryl, substituted orunsubstituted aralkyl, or substituted or unsubstituted heteroaralkyl.52. The method of claim 51, wherein R is:


53. The method of claim 51, wherein R¹ is hydrogen or methyl; n is 0; Eis:

wherein: Ra, Rb, and Rc are independently hydrogen, halogen, —CN,substituted or unsubstituted C₁-C₃ alkyl, substituted or unsubstitutedheteroalkyl, or substituted or unsubstituted cycloalkyl.
 54. The methodof claim 53, wherein -L-E is


55. The method of claim 51, wherein E is


56. The method of claim 51, wherein —X—Y is: (a) —CH₂—NH—Y, where Y ishydrogen, halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocyclyl, substituted or unsubstitutedaryl, substituted or unsubstituted heteroaryl, substituted orunsubstituted aralkyl, or substituted or unsubstituted heteroaralkyl; or(b) —CH₂—NR²—Y, where R² is hydrogen, lower alkyl, or lower cycloalkyl;and Y is hydrogen, halogen, substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedalkynyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, substituted or unsubstituted aralkyl, or substituted orunsubstituted heteroaralkyl; or (c) —C(O)—NR²—Y, where R² is hydrogen,lower alkyl, or lower cycloalkyl; and Y is selected from the groupconsisting of: hydrogen, halogen, substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedalkynyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, substituted or unsubstituted aralkyl, and substituted orunsubstituted heteroaralkyl; or (d) —NR²C(O)—Y, where R² is hydrogen,lower alkyl, or lower cycloalkyl; and Y is hydrogen, halogen,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocyclyl, substituted or unsubstitutedaryl, substituted or unsubstituted heteroaryl, substituted orunsubstituted aralkyl, or substituted or unsubstituted heteroaralkyl; or(e) —NR²SO₂—Y, where R² is hydrogen, lower alkyl, or lower cycloalkyl;and Y is hydrogen, halogen, substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedalkynyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, substituted or unsubstituted aralkyl, or substituted orunsubstituted heteroaralkyl; or (f) —O—CH₂—Y, where Y is hydrogen,halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocyclyl, substituted or unsubstitutedaryl, substituted or unsubstituted heteroaryl, substituted orunsubstituted aralkyl, or substituted or unsubstituted heteroaralkyl; or(g) —CH₂—NR³—Y, where R³ is —C(O)R⁴, —C(O)OR⁴ or —S(O)_(m)R⁴, wherein mis 1 or 2; R⁴ is lower alkyl or lower cycloalkyl; and Y is hydrogen,halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocyclyl, substituted or unsubstitutedaryl, substituted or unsubstituted heteroaryl, substituted orunsubstituted aralkyl, or substituted or unsubstituted heteroaralkyl; or(h) —CH₂—Y where Y is hydrogen, halogen, substituted or unsubstitutedalkyl, substituted or unsubstituted alkenyl, substituted orunsubstituted alkynyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocyclyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted aralkyl, orsubstituted or unsubstituted heteroaralkyl.
 57. The method of claim 51,wherein the method comprises administering to the subject in needthereof a therapeutically effective amount of a compound having thestructure of Formula IIa:

or a pharmaceutically acceptable salt, stereoisomer, tautomer, isotope,prodrug, or complex thereof, wherein R is substituted or unsubstitutedthiophenyl; m is 0, 1, 2 or 3; n₂ is 1, 2 or 3; R¹ is hydrogen, loweralkyl or lower cycloalkyl; and —X—Y is —CH₂—NH—Y, —CH₂—NR²—Y,—CH₂—NR³—Y, —NR²C(O)—Y, —C(O)NR²—Y, or —CH₂—Y, wherein R² is hydrogen,lower alkyl, or lower cycloalkyl; R³ is —C(O)R⁴, —C(O)OR⁴ or—S(O)_(m)R⁴, wherein m is 1 or 2; R⁴ is lower alkyl or lower cycloalkyl;and Y is hydrogen, halogen, substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedalkynyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, substituted or unsubstituted aralkyl, or substituted orunsubstituted heteroaralkyl.
 58. The method of claim 51, wherein themethod comprises administering to the subject in need thereof atherapeutically effective amount of a compound having one of thefollowing structures: Compound No. Structure  1

 3

 6

18

58

62

63

64

65

68

70

71

81

or a pharmaceutically acceptable salt, stereoisomer, tautomer, isotope,prodrug, or complex thereof.
 59. The method of claim 51, wherein the atleast one kinase member of the Tec kinase family is ITK, BTK, BMX, RLK,or a combination thereof.
 60. The method of claim 51, further comprisingadministering a therapeutically effective amount of at least oneadditional active pharmaceutical ingredient for the treatment of cancer,an autoimmune disease, an allergic disease, an inflammatory disease, ora viral infection.
 61. The method of claim 51, wherein the proteinkinase mediated disease, disorder, or condition is cancer, an autoimmunedisease, an allergic disease, an inflammatory disease, or a viralinfection.
 62. The method of any one of claims 51-61, wherein theprotein kinase mediated disease, disorder, or condition is lunginflammation, allergic asthma, pneumonia, psoriasis, atopic dermatitis,uveitis, dry eye disease, arthritis, systemic lupus erythematosus,rheumatoid arthritis, psoriatic arthritis, Still's disease, juvenilearthritis, type I diabetes, inflammatory bowel disease, myastheniagravis, Hashimoto's thyroiditis, Ord's thyroiditis, Basedow's disease,Sjogren's syndrome, multiple sclerosis, Guillain-Barre syndrome, acutedisseminated encephalomyelitis, Addison disease, opsoclonus-myoclonussyndrome, ankylosing spondylitis, antiphospholipid antibody syndrome,aplastic anemia, autoimmune hepatitis, celiac disease, Goodpasture'ssyndrome, idiopathic thrombocytopenic purpura, optic neuritis,scleroderma, primary biliary cirrhosis, Reiter's disease, Takayasuarteritis, temporal arteritis, warm autoimmune hemolytic anemia, Wegenergranuloma, alopecia universalis, Burchett disease, chronic fatiguesyndrome, dysautonomia, endometriosis, interstitial cystitis, myotonia,vulvodynia, pemphigus, allergy, anaphylaxis, allergic conjunctivitis,allergic rhinitis, atopic dermatitis, asthma, appendicitis, blepharitis,bronchiolitis, bronchitis, bursitis, cervicitis, cholangitis,cholecystitis, colitis, conjunctivitis, cystitis, dacryoadenitis,dermatitis, dermatomyositis, encephalitis, endocarditis, endometritis,enteritis, epicondylitis, epididymitis, fasciitis, fibrositis,gastritis, gastroenteritis, hepatitis, hidradenitis suppurativa,inflammatory bowel disease, laryngitis, mastitis, meningitis, myelitis,myocarditis, myositis nephritis, oophoritis, orchitis, osteitis,osteoarthritis, pancreatitis, parotitis, pericarditis, peritonitis,pharyngitis, pleuritis, phlebitis, pneumonia, proctitis, prostatitis,pyelonephritis, rhinitis, salpingitis, sinusitis, stomatitis, synovitis,tendinitis, tonsillitis, uveitis, vaginitis, vasculitis, vulvitis,HIV/AIDS, influenza, T-cell lymphomas, T-cell leukemias, peripheralT-cell lymphoma, Seazry syndrome/cutaneous T-cell lymphoma, acutelymphoblastic leukemia, adult T-cell leukemia/lymphoma, NK/T-celllymphoma, nasal type or aggressive NK-cell leukemia, or a combinationthereof.
 63. A method of modulating or inhibiting in a subject proteinkinase activity associated with at least one kinase member of the Teckinase family, comprising administering to the subject in need thereof atherapeutically effective amount of a compound of Formula 1:

or a pharmaceutically acceptable salt, stereoisomer, tautomer, isotope,prodrug, or complex thereof, wherein R is substituted or unsubstitutedthiophenyl; L is

wherein ring B₁ is substituted or unsubstituted cycloalkyl; R¹ ishydrogen, lower alkyl, or lower cycloalkyl; and n is 0 or 1; E is:

wherein: Ra, Rb, and Rc are independently hydrogen, halogen, —CN,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, or substituted orunsubstituted heterocyclyl; or Ra and Rb, taken together with the carbonatoms to which they are attached, form a 3- to 8-membered substituted orunsubstituted cycloalkyl ring or form a 3- to 8-membered substituted orunsubstituted heterocyclic ring and Rc is selected as above; or Rb andRc, taken together with the carbon atom to which they are attached, forma 3- to 8-membered substituted or unsubstituted cycloalkyl ring or forma 3- to 8-substituted or unsubstituted membered heterocyclic ring and Rais selected as above; or Ra and Rb, taken together with the carbon atomsto which they are attached, form a triple bond and Rc is selected asabove; wherein -L-E is:

X is a bond, alkylene, -(alkylene)-NR²—, -(alkylene)-NR³—,-(alkylene)-O—, —O—, —S—, —S(O)_(m)—, —NR²—, —NR³—, —C(O)—, —C(O)O—,—C(O)NR²—, —C(O)ONR²—, or S(O)_(m)NR²—, wherein: R² is hydrogen, loweralkyl or lower cycloalkyl; R³ is —C(O)R⁴, —C(O)OR⁴ or —S(O)_(m)R⁴; R⁴ islower alkyl or lower cycloalkyl; m is 1 or 2; and Y is hydrogen,halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocyclyl, substituted or unsubstitutedaryl, substituted or unsubstituted heteroaryl, substituted orunsubstituted aralkyl, or substituted or unsubstituted heteroaralkyl.64. A method of inhibiting in a cell or a tissue a protein kinaseassociated with at least one kinase member of the Tec kinase family,comprising contacting the cell or tissue with a compound of Formula 1:

or a pharmaceutically acceptable salt, stereoisomer, tautomer, isotope,prodrug, or complex thereof, wherein R is substituted or unsubstitutedthiophenyl; L is

wherein ring B₁ is substituted or unsubstituted cycloalkyl; R¹ ishydrogen, lower alkyl, or lower cycloalkyl; and n is 0 or 1; E is:

wherein: Ra, Rb, and Rc are independently hydrogen, halogen, —CN,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, or substituted orunsubstituted heterocyclyl; or Ra and Rb, taken together with the carbonatoms to which they are attached, form a 3- to 8-membered substituted orunsubstituted cycloalkyl ring or form a 3- to 8-membered substituted orunsubstituted heterocyclic ring and Rc is selected as above; or Rb andRc, taken together with the carbon atom to which they are attached, forma 3- to 8-membered substituted or unsubstituted cycloalkyl ring or forma 3- to 8-substituted or unsubstituted membered heterocyclic ring and Rais selected as above; or Ra and Rb, taken together with the carbon atomsto which they are attached, form a triple bond and Rc is selected asabove; wherein -L-E is:

X is a bond, alkylene, -(alkylene)-NR²—, -(alkylene)-NR³—,-(alkylene)-O—, —O—, —S—, —S(O)_(m)—, —NR²—, —NR³—, —C(O)—, —C(O)O—,—C(O)NR²—, —C(O)ONR²—, or S(O)_(m)NR²—, wherein: R² is hydrogen, loweralkyl or lower cycloalkyl; R³ is —C(O)R⁴, —C(O)OR⁴ or —S(O)_(m)R⁴; R⁴ islower alkyl or lower cycloalkyl; m is 1 or 2; and Y is hydrogen,halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocyclyl, substituted or unsubstitutedaryl, substituted or unsubstituted heteroaryl, substituted orunsubstituted aralkyl, or substituted or unsubstituted heteroaralkyl.